Starting phenix.real_space_refine on Tue Aug 26 06:02:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.map" model { file = "/net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zno_60275/08_2025/8zno_60275.cif" } resolution = 3.02 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= 0.007 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 10 7.16 5 Zn 2 6.06 5 P 26 5.49 5 S 148 5.16 5 C 22226 2.51 5 N 5716 2.21 5 O 6319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34447 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3502 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3855 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain: "C" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3076 Classifications: {'peptide': 386} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 354} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1893 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 224} Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 180} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 986 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 573 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "H" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "J" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'TRANS': 59} Chain: "K" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "M" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3502 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 432} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3855 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 463} Chain: "O" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3068 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 353} Chain: "P" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1893 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 224} Chain: "Q" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 180} Chain: "R" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 986 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "S" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 573 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "T" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "V" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'TRANS': 59} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {' ZN': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "C" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 335 Unusual residues: {'3PE': 6, 'CDL': 1, 'HEM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {' ZN': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "O" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 263 Unusual residues: {'3PE': 1, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 74 Chain: "P" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13423 SG CYS E 211 98.269 67.684 39.607 1.00115.00 S ATOM 13563 SG CYS E 230 97.893 71.437 39.509 1.00123.77 S ATOM 30059 SG CYS Q 211 36.230 84.514 40.494 1.00120.45 S ATOM 30199 SG CYS Q 230 36.374 80.583 41.119 1.00131.98 S ATOM 30199 SG CYS Q 230 36.374 80.583 41.119 1.00131.98 S Time building chain proxies: 6.26, per 1000 atoms: 0.18 Number of scatterers: 34447 At special positions: 0 Unit cell: (133.44, 155.52, 175.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 10 26.01 S 148 16.00 P 26 15.00 O 6319 8.00 N 5716 7.00 C 22226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS E 232 " distance=2.03 Simple disulfide: pdb=" SG CYS H 38 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 66 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 216 " - pdb=" SG CYS Q 232 " distance=2.04 Simple disulfide: pdb=" SG CYS T 38 " - pdb=" SG CYS T 80 " distance=2.04 Simple disulfide: pdb=" SG CYS T 42 " - pdb=" SG CYS T 76 " distance=2.03 Simple disulfide: pdb=" SG CYS T 52 " - pdb=" SG CYS T 66 " distance=2.04 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 230 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 211 " pdb="FE2 FES E 301 " - pdb=" ND1 HIS E 213 " pdb=" FES Q 301 " pdb="FE1 FES Q 301 " - pdb=" SG CYS Q 230 " pdb="FE1 FES Q 301 " - pdb=" SG CYS Q 211 " pdb="FE2 FES Q 301 " - pdb=" ND1 HIS Q 213 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 140 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 144 " pdb=" ZN N 601 " pdb="ZN ZN N 601 " - pdb=" NE2 HIS N 140 " pdb="ZN ZN N 601 " - pdb=" NE2 HIS N 144 " 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7846 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 23 sheets defined 55.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.886A pdb=" N PHE A 119 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.797A pdb=" N LEU A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.700A pdb=" N GLU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 223 removed outlier: 3.535A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.712A pdb=" N ALA A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 268 through 281 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.512A pdb=" N GLY A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 400 through 417 Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.541A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.726A pdb=" N TYR A 501 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.740A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.838A pdb=" N LEU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.628A pdb=" N PHE B 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 131 " --> pdb=" O SER B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 154 through 166 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.826A pdb=" N GLU B 225 " --> pdb=" O MET B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.683A pdb=" N PHE B 241 " --> pdb=" O HIS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 261 through 273 removed outlier: 3.744A pdb=" N LEU B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.882A pdb=" N LEU B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 377 through 385 Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.202A pdb=" N ALA B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.506A pdb=" N VAL B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 470 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 487 through 499 Processing helix chain 'B' and resid 517 through 524 removed outlier: 3.596A pdb=" N PHE B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 13 removed outlier: 3.636A pdb=" N LYS C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Proline residue: C 12 - end of helix Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 35 through 55 Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.606A pdb=" N VAL C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 107 removed outlier: 4.534A pdb=" N SER C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 removed outlier: 3.787A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.535A pdb=" N PHE C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 161 through 171 Processing helix chain 'C' and resid 176 through 207 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 229 through 251 removed outlier: 3.518A pdb=" N ALA C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.583A pdb=" N ASN C 260 " --> pdb=" O HIS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.873A pdb=" N VAL C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 319 through 322 removed outlier: 3.736A pdb=" N PHE C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 323 through 344 Processing helix chain 'C' and resid 353 through 370 Proline residue: C 359 - end of helix removed outlier: 4.192A pdb=" N PHE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 370 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 removed outlier: 4.024A pdb=" N GLY C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.572A pdb=" N THR C 385 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.500A pdb=" N VAL D 118 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 removed outlier: 4.099A pdb=" N ILE D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 188 through 198 Processing helix chain 'D' and resid 244 through 261 Processing helix chain 'D' and resid 263 through 298 removed outlier: 4.882A pdb=" N VAL D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU D 296 " --> pdb=" O ARG D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.822A pdb=" N ALA E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 133 removed outlier: 3.858A pdb=" N GLY E 114 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.845A pdb=" N LEU E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'F' and resid 15 through 31 removed outlier: 3.925A pdb=" N ALA F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN F 20 " --> pdb=" O TRP F 16 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.542A pdb=" N LEU F 39 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 40 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.675A pdb=" N ASP F 45 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 54 Processing helix chain 'F' and resid 56 through 77 removed outlier: 3.606A pdb=" N VAL F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 87 Processing helix chain 'F' and resid 95 through 112 removed outlier: 3.576A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.795A pdb=" N GLY G 43 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 88 removed outlier: 3.613A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) Proline residue: G 69 - end of helix Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.504A pdb=" N TYR H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 66 through 89 removed outlier: 4.513A pdb=" N GLN H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS H 84 " --> pdb=" O CYS H 80 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER H 87 " --> pdb=" O GLN H 83 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 21 Processing helix chain 'J' and resid 24 through 54 removed outlier: 4.625A pdb=" N ARG J 40 " --> pdb=" O PHE J 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN J 54 " --> pdb=" O TRP J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.847A pdb=" N ILE J 62 " --> pdb=" O TYR J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 33 Processing helix chain 'M' and resid 120 through 128 removed outlier: 3.977A pdb=" N LEU M 124 " --> pdb=" O GLY M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 149 Processing helix chain 'M' and resid 171 through 185 Processing helix chain 'M' and resid 189 through 205 Processing helix chain 'M' and resid 210 through 223 Processing helix chain 'M' and resid 226 through 230 Processing helix chain 'M' and resid 235 through 242 Processing helix chain 'M' and resid 243 through 255 removed outlier: 3.597A pdb=" N LEU M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 258 No H-bonds generated for 'chain 'M' and resid 256 through 258' Processing helix chain 'M' and resid 268 through 281 removed outlier: 3.661A pdb=" N LEU M 272 " --> pdb=" O GLU M 268 " (cutoff:3.500A) Proline residue: M 278 - end of helix Processing helix chain 'M' and resid 330 through 345 Processing helix chain 'M' and resid 361 through 368 Processing helix chain 'M' and resid 400 through 417 Processing helix chain 'M' and resid 422 through 441 Processing helix chain 'M' and resid 443 through 458 Processing helix chain 'M' and resid 463 through 473 removed outlier: 3.699A pdb=" N PHE M 467 " --> pdb=" O PRO M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 487 Processing helix chain 'M' and resid 504 through 512 removed outlier: 3.606A pdb=" N VAL M 508 " --> pdb=" O ASN M 504 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS M 511 " --> pdb=" O SER M 507 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE M 512 " --> pdb=" O VAL M 508 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 67 removed outlier: 3.502A pdb=" N ARG N 55 " --> pdb=" O MET N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 127 through 131 removed outlier: 3.696A pdb=" N PHE N 130 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU N 131 " --> pdb=" O SER N 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 127 through 131' Processing helix chain 'N' and resid 137 through 146 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'N' and resid 154 through 166 removed outlier: 3.605A pdb=" N MET N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY N 166 " --> pdb=" O ILE N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.621A pdb=" N ALA N 192 " --> pdb=" O ASP N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 223 Processing helix chain 'N' and resid 228 through 241 removed outlier: 3.543A pdb=" N PHE N 241 " --> pdb=" O HIS N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 248 Processing helix chain 'N' and resid 253 through 258 removed outlier: 4.055A pdb=" N LYS N 258 " --> pdb=" O ALA N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 273 removed outlier: 3.743A pdb=" N LEU N 265 " --> pdb=" O THR N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 299 Processing helix chain 'N' and resid 309 through 314 Processing helix chain 'N' and resid 350 through 360 Processing helix chain 'N' and resid 376 through 386 Processing helix chain 'N' and resid 414 through 433 removed outlier: 4.263A pdb=" N ALA N 430 " --> pdb=" O THR N 426 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL N 433 " --> pdb=" O LEU N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 453 removed outlier: 4.033A pdb=" N ILE N 453 " --> pdb=" O LEU N 449 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 470 Processing helix chain 'N' and resid 475 through 484 removed outlier: 3.556A pdb=" N LEU N 479 " --> pdb=" O PRO N 475 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 499 Processing helix chain 'N' and resid 517 through 524 removed outlier: 3.519A pdb=" N PHE N 521 " --> pdb=" O ASP N 517 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 13 No H-bonds generated for 'chain 'O' and resid 11 through 13' Processing helix chain 'O' and resid 14 through 22 Processing helix chain 'O' and resid 31 through 34 removed outlier: 3.515A pdb=" N TRP O 34 " --> pdb=" O SER O 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 31 through 34' Processing helix chain 'O' and resid 35 through 55 Processing helix chain 'O' and resid 64 through 76 removed outlier: 3.575A pdb=" N VAL O 76 " --> pdb=" O VAL O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 107 removed outlier: 3.713A pdb=" N LEU O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 136 Processing helix chain 'O' and resid 141 through 154 Processing helix chain 'O' and resid 155 through 157 No H-bonds generated for 'chain 'O' and resid 155 through 157' Processing helix chain 'O' and resid 161 through 171 Processing helix chain 'O' and resid 176 through 207 Proline residue: O 191 - end of helix Processing helix chain 'O' and resid 229 through 251 removed outlier: 3.797A pdb=" N ALA O 251 " --> pdb=" O TRP O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 257 through 262 Processing helix chain 'O' and resid 276 through 278 No H-bonds generated for 'chain 'O' and resid 276 through 278' Processing helix chain 'O' and resid 279 through 289 removed outlier: 4.083A pdb=" N ILE O 289 " --> pdb=" O ILE O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 291 through 309 removed outlier: 4.087A pdb=" N ILE O 299 " --> pdb=" O GLY O 295 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA O 300 " --> pdb=" O VAL O 296 " (cutoff:3.500A) Proline residue: O 301 - end of helix Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 319 through 322 Processing helix chain 'O' and resid 323 through 344 removed outlier: 3.696A pdb=" N GLY O 341 " --> pdb=" O ARG O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 370 Proline residue: O 359 - end of helix removed outlier: 4.280A pdb=" N PHE O 367 " --> pdb=" O PHE O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 370 through 378 removed outlier: 3.748A pdb=" N GLY O 374 " --> pdb=" O THR O 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 103 Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 123 through 134 removed outlier: 3.608A pdb=" N VAL P 127 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE P 134 " --> pdb=" O MET P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 170 Processing helix chain 'P' and resid 188 through 199 Processing helix chain 'P' and resid 244 through 261 Processing helix chain 'P' and resid 263 through 294 Processing helix chain 'P' and resid 295 through 299 removed outlier: 3.576A pdb=" N SER P 298 " --> pdb=" O VAL P 295 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG P 299 " --> pdb=" O LEU P 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 295 through 299' Processing helix chain 'Q' and resid 104 through 111 Processing helix chain 'Q' and resid 112 through 133 removed outlier: 3.555A pdb=" N ALA Q 120 " --> pdb=" O ARG Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 143 removed outlier: 3.703A pdb=" N LEU Q 143 " --> pdb=" O ASP Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 182 Processing helix chain 'Q' and resid 194 through 199 Processing helix chain 'R' and resid 16 through 33 removed outlier: 3.922A pdb=" N GLN R 20 " --> pdb=" O TRP R 16 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE R 32 " --> pdb=" O ARG R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 39 removed outlier: 3.509A pdb=" N LEU R 39 " --> pdb=" O TYR R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 55 removed outlier: 3.796A pdb=" N GLU R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 77 removed outlier: 3.558A pdb=" N VAL R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 Processing helix chain 'R' and resid 95 through 112 removed outlier: 3.623A pdb=" N LEU R 112 " --> pdb=" O GLU R 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 89 removed outlier: 5.560A pdb=" N ILE S 61 " --> pdb=" O SER S 57 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER S 62 " --> pdb=" O GLU S 58 " (cutoff:3.500A) Proline residue: S 69 - end of helix removed outlier: 3.617A pdb=" N ARG S 89 " --> pdb=" O LYS S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 36 removed outlier: 3.634A pdb=" N TYR T 33 " --> pdb=" O ASP T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 57 Processing helix chain 'T' and resid 66 through 89 removed outlier: 5.155A pdb=" N GLN T 83 " --> pdb=" O LYS T 79 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS T 84 " --> pdb=" O CYS T 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 21 Processing helix chain 'V' and resid 24 through 54 removed outlier: 3.791A pdb=" N ASN V 54 " --> pdb=" O TRP V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 62 removed outlier: 3.658A pdb=" N ASP V 61 " --> pdb=" O ARG V 58 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE V 62 " --> pdb=" O TYR V 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 58 through 62' Processing helix chain 'W' and resid 11 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.614A pdb=" N LYS A 90 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 166 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 removed outlier: 6.627A pdb=" N TYR A 301 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 492 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 494 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 392 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.738A pdb=" N ARG B 97 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 109 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG B 106 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA B 282 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 108 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY B 284 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.572A pdb=" N SER B 390 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 404 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 394 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.572A pdb=" N SER B 390 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 324 " --> pdb=" O GLY G 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'D' and resid 135 through 140 removed outlier: 3.878A pdb=" N PHE D 147 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 214 through 215 Processing sheet with id=AA9, first strand: chain 'E' and resid 95 through 96 removed outlier: 3.979A pdb=" N GLU E 95 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 168 through 169 Processing sheet with id=AB2, first strand: chain 'E' and resid 219 through 220 removed outlier: 3.704A pdb=" N TRP E 228 " --> pdb=" O TYR E 237 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS E 236 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS E 245 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP E 238 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE E 243 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 81 through 84 removed outlier: 3.798A pdb=" N ILE M 81 " --> pdb=" O SER M 93 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS M 90 " --> pdb=" O LEU M 262 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA M 264 " --> pdb=" O LYS M 90 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA M 92 " --> pdb=" O ALA M 264 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA M 263 " --> pdb=" O GLY M 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 299 through 304 removed outlier: 6.495A pdb=" N GLY M 299 " --> pdb=" O MET M 493 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER M 495 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR M 301 " --> pdb=" O SER M 495 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY M 497 " --> pdb=" O TYR M 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS M 303 " --> pdb=" O GLY M 497 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR M 492 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA M 494 " --> pdb=" O ALA M 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 299 through 304 removed outlier: 6.495A pdb=" N GLY M 299 " --> pdb=" O MET M 493 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N SER M 495 " --> pdb=" O GLY M 299 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR M 301 " --> pdb=" O SER M 495 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY M 497 " --> pdb=" O TYR M 301 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS M 303 " --> pdb=" O GLY M 497 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR M 492 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA M 494 " --> pdb=" O ALA M 319 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU M 324 " --> pdb=" O GLY M 388 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY M 388 " --> pdb=" O LEU M 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY M 391 " --> pdb=" O PHE M 380 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE M 380 " --> pdb=" O GLY M 391 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 97 through 98 removed outlier: 3.914A pdb=" N ARG N 106 " --> pdb=" O MET N 278 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY N 284 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR N 180 " --> pdb=" O VAL N 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 364 through 365 removed outlier: 3.562A pdb=" N SER N 390 " --> pdb=" O VAL N 409 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE N 404 " --> pdb=" O PHE N 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 364 through 365 removed outlier: 3.562A pdb=" N SER N 390 " --> pdb=" O VAL N 409 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 26 through 27 Processing sheet with id=AC1, first strand: chain 'P' and resid 135 through 140 removed outlier: 3.963A pdb=" N PHE P 147 " --> pdb=" O ASP P 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 214 through 215 Processing sheet with id=AC3, first strand: chain 'Q' and resid 95 through 96 removed outlier: 3.691A pdb=" N GLU Q 95 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 168 through 169 Processing sheet with id=AC5, first strand: chain 'Q' and resid 229 through 230 1738 hydrogen bonds defined for protein. 4995 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: 5.61 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 10944 1.35 - 1.57: 24051 1.57 - 1.78: 65 1.78 - 1.99: 233 1.99 - 2.21: 32 Bond restraints: 35325 Sorted by residual: bond pdb=" C ALA Q 108 " pdb=" O ALA Q 108 " ideal model delta sigma weight residual 1.235 1.139 0.096 1.26e-02 6.30e+03 5.84e+01 bond pdb=" CB7 CDL O 402 " pdb=" OB8 CDL O 402 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.86e+01 bond pdb=" CB7 CDL P 404 " pdb=" OB8 CDL P 404 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.85e+01 bond pdb=" CB7 CDL B 602 " pdb=" OB8 CDL B 602 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.77e+01 bond pdb=" CA7 CDL O 402 " pdb=" OA8 CDL O 402 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.61e+01 ... (remaining 35320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 46774 2.96 - 5.92: 1010 5.92 - 8.88: 106 8.88 - 11.84: 24 11.84 - 14.81: 15 Bond angle restraints: 47929 Sorted by residual: angle pdb=" N PHE R 17 " pdb=" CA PHE R 17 " pdb=" C PHE R 17 " ideal model delta sigma weight residual 111.04 96.73 14.31 1.55e+00 4.16e-01 8.52e+01 angle pdb=" C11 CDL O 405 " pdb=" CA5 CDL O 405 " pdb=" OA6 CDL O 405 " ideal model delta sigma weight residual 111.33 120.94 -9.61 1.32e+00 5.72e-01 5.29e+01 angle pdb=" C11 CDL D 401 " pdb=" CA5 CDL D 401 " pdb=" OA6 CDL D 401 " ideal model delta sigma weight residual 111.33 120.89 -9.56 1.32e+00 5.72e-01 5.23e+01 angle pdb=" C11 CDL B 602 " pdb=" CA5 CDL B 602 " pdb=" OA6 CDL B 602 " ideal model delta sigma weight residual 111.33 120.63 -9.30 1.32e+00 5.72e-01 4.95e+01 angle pdb=" C51 CDL B 602 " pdb=" CB5 CDL B 602 " pdb=" OB6 CDL B 602 " ideal model delta sigma weight residual 111.33 120.33 -9.00 1.32e+00 5.72e-01 4.63e+01 ... (remaining 47924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.91: 20326 30.91 - 61.83: 843 61.83 - 92.74: 81 92.74 - 123.66: 0 123.66 - 154.57: 2 Dihedral angle restraints: 21252 sinusoidal: 9021 harmonic: 12231 Sorted by residual: dihedral pdb=" CA PRO C 159 " pdb=" C PRO C 159 " pdb=" N VAL C 160 " pdb=" CA VAL C 160 " ideal model delta harmonic sigma weight residual -180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CB CYS T 42 " pdb=" SG CYS T 42 " pdb=" SG CYS T 76 " pdb=" CB CYS T 76 " ideal model delta sinusoidal sigma weight residual 93.00 155.16 -62.16 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CA PRO O 159 " pdb=" C PRO O 159 " pdb=" N VAL O 160 " pdb=" CA VAL O 160 " ideal model delta harmonic sigma weight residual -180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 21249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 5003 0.116 - 0.232: 129 0.232 - 0.348: 1 0.348 - 0.464: 0 0.464 - 0.580: 1 Chirality restraints: 5134 Sorted by residual: chirality pdb=" CA TYR Q 109 " pdb=" N TYR Q 109 " pdb=" C TYR Q 109 " pdb=" CB TYR Q 109 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" CA4 CDL N 602 " pdb=" CA3 CDL N 602 " pdb=" CA6 CDL N 602 " pdb=" OA6 CDL N 602 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB4 CDL O 405 " pdb=" CB3 CDL O 405 " pdb=" CB6 CDL O 405 " pdb=" OB6 CDL O 405 " both_signs ideal model delta sigma weight residual False -2.57 -2.35 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 5131 not shown) Planarity restraints: 6069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 402 " 0.024 2.00e-02 2.50e+03 7.42e-02 1.24e+02 pdb=" C2C HEC D 402 " -0.203 2.00e-02 2.50e+03 pdb=" C3C HEC D 402 " 0.027 2.00e-02 2.50e+03 pdb=" C4C HEC D 402 " 0.004 2.00e-02 2.50e+03 pdb=" CAC HEC D 402 " 0.039 2.00e-02 2.50e+03 pdb=" CHC HEC D 402 " 0.040 2.00e-02 2.50e+03 pdb=" CHD HEC D 402 " -0.000 2.00e-02 2.50e+03 pdb=" CMC HEC D 402 " 0.062 2.00e-02 2.50e+03 pdb=" NC HEC D 402 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA P 185 " -0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO P 186 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO P 186 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO P 186 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 489 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO M 490 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO M 490 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 490 " 0.050 5.00e-02 4.00e+02 ... (remaining 6066 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 186 2.53 - 3.12: 25373 3.12 - 3.72: 50170 3.72 - 4.31: 69133 4.31 - 4.90: 119783 Nonbonded interactions: 264645 Sorted by model distance: nonbonded pdb=" O PHE R 17 " pdb=" N ALA R 19 " model vdw 1.939 3.120 nonbonded pdb=" OH TYR O 316 " pdb=" OD2 ASP R 45 " model vdw 2.105 3.040 nonbonded pdb=" OD1 ASN R 15 " pdb=" N TRP R 16 " model vdw 2.110 3.120 nonbonded pdb=" OD1 ASN R 15 " pdb=" N PHE R 17 " model vdw 2.143 3.120 nonbonded pdb=" OD1 ASP O 176 " pdb=" N ASN O 177 " model vdw 2.152 3.120 ... (remaining 264640 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 'M' } ncs_group { reference = (chain 'B' and (resid 44 through 601 or (resid 602 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C51 \ or name C52 or name C53 or name C54 or name C55 or name C56 or name C71 or name \ C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or name CA3 or n \ ame CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 \ or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name O \ A6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or na \ me OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) selection = (chain 'N' and (resid 44 through 601 or (resid 602 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C51 \ or name C52 or name C53 or name C54 or name C55 or name C56 or name C71 or name \ C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or name CA3 or n \ ame CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or name CB6 \ or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name O \ A6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name OB6 or na \ me OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) } ncs_group { reference = (chain 'C' and (resid 1 through 385 or (resid 405 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) selection = (chain 'O' and (resid 1 through 385 or (resid 401 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } ncs_group { reference = (chain 'D' and resid 66 through 307) selection = (chain 'P' and resid 66 through 307) } ncs_group { reference = (chain 'E' and resid 72 through 301) selection = chain 'Q' } ncs_group { reference = chain 'F' selection = (chain 'R' and resid 7 through 123) } ncs_group { reference = chain 'G' selection = (chain 'S' and (resid 21 through 90 or (resid 101 and (name N or name C1 or name \ C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } ncs_group { reference = chain 'H' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } 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: 1.340 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.000 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.011 1.028 35349 Z= 0.397 Angle : 1.029 29.039 47951 Z= 0.510 Chirality : 0.049 0.580 5134 Planarity : 0.006 0.121 6069 Dihedral : 16.050 154.572 13382 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.55 % Favored : 93.35 % Rotamer: Outliers : 0.11 % Allowed : 0.42 % Favored : 99.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: -0.94 (0.13), residues: 4181 helix: 0.59 (0.11), residues: 2114 sheet: -1.71 (0.25), residues: 406 loop : -1.93 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 149 TYR 0.038 0.002 TYR R 118 PHE 0.046 0.002 PHE C 93 TRP 0.057 0.002 TRP O 34 HIS 0.013 0.001 HIS O 188 Details of bonding type rmsd covalent geometry : bond 0.00672 (35325) covalent geometry : angle 1.00401 (47929) SS BOND : bond 0.00547 ( 8) SS BOND : angle 2.58914 ( 16) hydrogen bonds : bond 0.16334 ( 1720) hydrogen bonds : angle 5.87021 ( 4995) metal coordination : bond 0.45986 ( 10) metal coordination : angle 19.84177 ( 6) Misc. bond : bond 0.35401 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 500 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7867 (pt) cc_final: 0.7654 (pp) REVERT: A 159 GLU cc_start: 0.7689 (tp30) cc_final: 0.6997 (mt-10) REVERT: A 239 LEU cc_start: 0.8351 (mp) cc_final: 0.8122 (mp) REVERT: B 331 GLU cc_start: 0.6666 (mp0) cc_final: 0.6409 (mp0) REVERT: C 375 ARG cc_start: 0.7381 (mpt-90) cc_final: 0.7068 (mmm160) REVERT: D 138 ASP cc_start: 0.7032 (t0) cc_final: 0.6749 (t70) REVERT: H 78 ASP cc_start: 0.8135 (m-30) cc_final: 0.7915 (m-30) REVERT: M 331 LEU cc_start: 0.8397 (tt) cc_final: 0.7147 (mp) REVERT: N 287 LYS cc_start: 0.8448 (tppt) cc_final: 0.8023 (tppp) REVERT: P 68 GLU cc_start: 0.6802 (pp20) cc_final: 0.5686 (tm-30) REVERT: P 241 THR cc_start: 0.8875 (m) cc_final: 0.8560 (m) REVERT: S 83 LYS cc_start: 0.6310 (tppp) cc_final: 0.5814 (tttt) REVERT: T 54 LYS cc_start: 0.7552 (pptt) cc_final: 0.7276 (ptmm) outliers start: 4 outliers final: 2 residues processed: 501 average time/residue: 0.1815 time to fit residues: 145.7234 Evaluate side-chains 400 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain R residue 14 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 136 ASN R 53 ASN V 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.173883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132598 restraints weight = 45724.650| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.44 r_work: 0.3387 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.192 35349 Z= 0.298 Angle : 0.848 27.898 47951 Z= 0.416 Chirality : 0.051 0.230 5134 Planarity : 0.007 0.096 6069 Dihedral : 14.458 132.301 5516 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.40 % Allowed : 8.56 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.00 (0.13), residues: 4181 helix: 0.50 (0.11), residues: 2131 sheet: -1.27 (0.27), residues: 354 loop : -2.05 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 287 TYR 0.025 0.002 TYR F 40 PHE 0.057 0.002 PHE C 93 TRP 0.022 0.002 TRP P 78 HIS 0.014 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00737 (35325) covalent geometry : angle 0.81984 (47929) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.68227 ( 16) hydrogen bonds : bond 0.08684 ( 1720) hydrogen bonds : angle 4.86228 ( 4995) metal coordination : bond 0.02958 ( 10) metal coordination : angle 19.28783 ( 6) Misc. bond : bond 0.13651 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 422 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7964 (tp30) cc_final: 0.6903 (mt-10) REVERT: A 239 LEU cc_start: 0.8298 (mp) cc_final: 0.7835 (mp) REVERT: D 229 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6493 (mtm) REVERT: G 41 MET cc_start: 0.7676 (mmt) cc_final: 0.7231 (mmt) REVERT: H 78 ASP cc_start: 0.8336 (m-30) cc_final: 0.8134 (m-30) REVERT: J 67 GLN cc_start: 0.6636 (mp10) cc_final: 0.6425 (mm110) REVERT: M 318 PHE cc_start: 0.8148 (p90) cc_final: 0.7553 (p90) REVERT: M 335 MET cc_start: 0.8018 (mpp) cc_final: 0.7751 (mpp) REVERT: M 360 TYR cc_start: 0.8090 (m-80) cc_final: 0.7518 (m-80) REVERT: O 219 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7281 (tm-30) REVERT: O 267 MET cc_start: 0.8115 (tmm) cc_final: 0.7765 (tmm) REVERT: P 68 GLU cc_start: 0.7234 (pp20) cc_final: 0.5791 (tm-30) REVERT: Q 109 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5588 (t80) REVERT: Q 121 SER cc_start: 0.8137 (m) cc_final: 0.7881 (m) REVERT: Q 122 LEU cc_start: 0.7555 (tt) cc_final: 0.7288 (tp) REVERT: S 58 GLU cc_start: 0.6516 (tm-30) cc_final: 0.5830 (tm-30) REVERT: S 83 LYS cc_start: 0.5850 (tppp) cc_final: 0.5326 (tttt) REVERT: T 48 GLU cc_start: 0.8207 (mp0) cc_final: 0.7725 (mp0) REVERT: T 54 LYS cc_start: 0.7742 (pptt) cc_final: 0.7486 (ptmm) REVERT: V 61 ASP cc_start: 0.8618 (m-30) cc_final: 0.8391 (m-30) outliers start: 50 outliers final: 37 residues processed: 448 average time/residue: 0.1789 time to fit residues: 130.6257 Evaluate side-chains 430 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 391 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 324 LEU Chi-restraints excluded: chain M residue 333 ASP Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 479 ILE Chi-restraints excluded: chain M residue 504 ASN Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 272 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 352 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 375 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS M 304 HIS V 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137103 restraints weight = 45459.827| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.26 r_work: 0.3457 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 35349 Z= 0.158 Angle : 0.686 24.392 47951 Z= 0.333 Chirality : 0.044 0.217 5134 Planarity : 0.006 0.069 6069 Dihedral : 13.632 127.970 5512 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.65 % Allowed : 11.67 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.44 (0.13), residues: 4181 helix: 1.00 (0.11), residues: 2131 sheet: -0.95 (0.28), residues: 344 loop : -1.85 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 54 TYR 0.018 0.001 TYR C 226 PHE 0.024 0.001 PHE C 93 TRP 0.016 0.001 TRP D 274 HIS 0.006 0.001 HIS S 88 Details of bonding type rmsd covalent geometry : bond 0.00361 (35325) covalent geometry : angle 0.66159 (47929) SS BOND : bond 0.00648 ( 8) SS BOND : angle 1.66853 ( 16) hydrogen bonds : bond 0.06406 ( 1720) hydrogen bonds : angle 4.41394 ( 4995) metal coordination : bond 0.02055 ( 10) metal coordination : angle 16.06373 ( 6) Misc. bond : bond 0.13163 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7841 (tp30) cc_final: 0.6866 (mt-10) REVERT: A 239 LEU cc_start: 0.8287 (mp) cc_final: 0.7844 (mp) REVERT: C 6 PHE cc_start: 0.8215 (m-80) cc_final: 0.7900 (m-80) REVERT: D 229 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6396 (mtm) REVERT: J 39 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: J 49 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6658 (tt) REVERT: M 318 PHE cc_start: 0.8177 (p90) cc_final: 0.7506 (p90) REVERT: M 335 MET cc_start: 0.7927 (mpp) cc_final: 0.7614 (mtm) REVERT: M 359 MET cc_start: 0.7382 (ttp) cc_final: 0.6373 (mmt) REVERT: N 244 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8441 (m) REVERT: O 219 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7197 (tm-30) REVERT: O 267 MET cc_start: 0.8057 (tmm) cc_final: 0.7628 (tmm) REVERT: O 375 ARG cc_start: 0.6529 (mmt180) cc_final: 0.6051 (tpp80) REVERT: Q 109 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5381 (t80) REVERT: S 83 LYS cc_start: 0.5709 (tppp) cc_final: 0.5188 (tttt) REVERT: T 50 GLN cc_start: 0.7890 (mt0) cc_final: 0.7381 (mp10) REVERT: V 39 GLU cc_start: 0.7264 (pt0) cc_final: 0.6935 (pt0) outliers start: 59 outliers final: 36 residues processed: 451 average time/residue: 0.1794 time to fit residues: 132.0793 Evaluate side-chains 424 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 504 ASN Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 264 MET Chi-restraints excluded: chain P residue 294 SER Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 360 optimal weight: 7.9990 chunk 380 optimal weight: 30.0000 chunk 386 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 82 optimal weight: 0.0030 chunk 73 optimal weight: 0.1980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 HIS B 444 GLN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN N 136 ASN N 519 ASN V 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140090 restraints weight = 45261.285| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.29 r_work: 0.3489 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 35349 Z= 0.131 Angle : 0.625 23.704 47951 Z= 0.305 Chirality : 0.043 0.226 5134 Planarity : 0.005 0.065 6069 Dihedral : 12.933 122.275 5512 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.96 % Allowed : 13.16 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.00 (0.13), residues: 4181 helix: 1.34 (0.11), residues: 2140 sheet: -0.57 (0.27), residues: 384 loop : -1.68 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 287 TYR 0.014 0.001 TYR M 360 PHE 0.015 0.001 PHE C 93 TRP 0.017 0.001 TRP P 274 HIS 0.006 0.001 HIS S 88 Details of bonding type rmsd covalent geometry : bond 0.00292 (35325) covalent geometry : angle 0.60251 (47929) SS BOND : bond 0.00214 ( 8) SS BOND : angle 1.78926 ( 16) hydrogen bonds : bond 0.05405 ( 1720) hydrogen bonds : angle 4.15385 ( 4995) metal coordination : bond 0.01837 ( 10) metal coordination : angle 14.56285 ( 6) Misc. bond : bond 0.10494 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 424 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7776 (tp30) cc_final: 0.6765 (mt-10) REVERT: C 6 PHE cc_start: 0.8186 (m-80) cc_final: 0.7855 (m-80) REVERT: C 375 ARG cc_start: 0.7486 (mpt-90) cc_final: 0.6496 (tpt170) REVERT: H 78 ASP cc_start: 0.8194 (m-30) cc_final: 0.7697 (m-30) REVERT: J 39 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: J 49 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6558 (tt) REVERT: M 159 GLU cc_start: 0.8007 (tp30) cc_final: 0.7686 (tp30) REVERT: M 318 PHE cc_start: 0.8188 (p90) cc_final: 0.7421 (p90) REVERT: M 359 MET cc_start: 0.6954 (ttp) cc_final: 0.5903 (mmt) REVERT: M 377 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7117 (tp) REVERT: N 244 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8438 (m) REVERT: O 267 MET cc_start: 0.7977 (tmm) cc_final: 0.7652 (tmm) REVERT: O 375 ARG cc_start: 0.6487 (mmt180) cc_final: 0.5987 (tpp80) REVERT: P 68 GLU cc_start: 0.7435 (pp20) cc_final: 0.6966 (pp20) REVERT: P 116 ASP cc_start: 0.7969 (m-30) cc_final: 0.7572 (t0) REVERT: Q 109 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5049 (t80) REVERT: S 83 LYS cc_start: 0.5712 (tppp) cc_final: 0.5170 (tttt) outliers start: 70 outliers final: 42 residues processed: 468 average time/residue: 0.1878 time to fit residues: 141.9536 Evaluate side-chains 434 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 387 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 294 SER Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 36 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 164 ASN ** M 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 312 ASN N 256 ASN V 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.173113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132266 restraints weight = 45387.445| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.58 r_work: 0.3366 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 35349 Z= 0.320 Angle : 0.837 25.393 47951 Z= 0.409 Chirality : 0.051 0.233 5134 Planarity : 0.006 0.069 6069 Dihedral : 13.419 120.632 5512 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.86 % Allowed : 14.50 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.58 (0.13), residues: 4181 helix: 0.80 (0.11), residues: 2137 sheet: -0.72 (0.29), residues: 324 loop : -1.87 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 68 TYR 0.025 0.002 TYR C 226 PHE 0.042 0.002 PHE C 93 TRP 0.019 0.003 TRP M 191 HIS 0.016 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00796 (35325) covalent geometry : angle 0.81875 (47929) SS BOND : bond 0.00361 ( 8) SS BOND : angle 2.37219 ( 16) hydrogen bonds : bond 0.08691 ( 1720) hydrogen bonds : angle 4.55666 ( 4995) metal coordination : bond 0.02176 ( 10) metal coordination : angle 15.04814 ( 6) Misc. bond : bond 0.19490 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 394 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7900 (tp30) cc_final: 0.6959 (mt-10) REVERT: A 318 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.6965 (p90) REVERT: B 331 GLU cc_start: 0.6987 (mp0) cc_final: 0.6662 (mp0) REVERT: H 78 ASP cc_start: 0.8291 (m-30) cc_final: 0.7872 (m-30) REVERT: J 39 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5790 (tt0) REVERT: J 49 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6631 (tt) REVERT: M 318 PHE cc_start: 0.8203 (p90) cc_final: 0.7454 (p90) REVERT: M 335 MET cc_start: 0.7764 (mpp) cc_final: 0.7516 (tpp) REVERT: M 359 MET cc_start: 0.7162 (ttp) cc_final: 0.6089 (mmt) REVERT: M 377 ILE cc_start: 0.7504 (tp) cc_final: 0.7302 (tp) REVERT: N 244 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8504 (m) REVERT: N 423 MET cc_start: 0.8867 (mmm) cc_final: 0.8595 (mmt) REVERT: O 267 MET cc_start: 0.8141 (tmm) cc_final: 0.7908 (tmm) REVERT: O 375 ARG cc_start: 0.6659 (mmt180) cc_final: 0.6102 (tpp80) REVERT: P 68 GLU cc_start: 0.7422 (pp20) cc_final: 0.6995 (pp20) REVERT: Q 109 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5626 (t80) REVERT: R 58 GLU cc_start: 0.8077 (mp0) cc_final: 0.7837 (mp0) REVERT: S 58 GLU cc_start: 0.6469 (tm-30) cc_final: 0.5927 (tm-30) REVERT: S 83 LYS cc_start: 0.5843 (tppp) cc_final: 0.5179 (tttt) outliers start: 102 outliers final: 69 residues processed: 464 average time/residue: 0.1708 time to fit residues: 129.9450 Evaluate side-chains 455 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 381 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 324 LEU Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 504 ASN Chi-restraints excluded: chain M residue 512 PHE Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 273 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 333 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 189 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 373 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 404 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 376 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 ASN V 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135634 restraints weight = 45174.776| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.39 r_work: 0.3423 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 35349 Z= 0.185 Angle : 0.695 22.807 47951 Z= 0.341 Chirality : 0.045 0.202 5134 Planarity : 0.006 0.066 6069 Dihedral : 13.008 117.733 5512 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.78 % Allowed : 15.40 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.30 (0.13), residues: 4181 helix: 1.07 (0.11), residues: 2139 sheet: -0.59 (0.29), residues: 330 loop : -1.78 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 120 TYR 0.017 0.002 TYR T 33 PHE 0.020 0.001 PHE C 93 TRP 0.019 0.002 TRP M 191 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00445 (35325) covalent geometry : angle 0.67719 (47929) SS BOND : bond 0.00671 ( 8) SS BOND : angle 2.12667 ( 16) hydrogen bonds : bond 0.06785 ( 1720) hydrogen bonds : angle 4.30818 ( 4995) metal coordination : bond 0.01711 ( 10) metal coordination : angle 13.72089 ( 6) Misc. bond : bond 0.13989 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 397 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7867 (tp30) cc_final: 0.6909 (mt-10) REVERT: A 318 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6919 (p90) REVERT: B 133 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6751 (mm-30) REVERT: B 331 GLU cc_start: 0.6926 (mp0) cc_final: 0.6566 (mp0) REVERT: B 389 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: C 6 PHE cc_start: 0.8266 (m-80) cc_final: 0.8019 (m-80) REVERT: H 78 ASP cc_start: 0.8426 (m-30) cc_final: 0.7964 (m-30) REVERT: J 39 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5646 (tt0) REVERT: J 49 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6519 (tt) REVERT: M 318 PHE cc_start: 0.8183 (p90) cc_final: 0.7448 (p90) REVERT: M 359 MET cc_start: 0.7012 (ttp) cc_final: 0.6006 (mmt) REVERT: M 377 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7270 (tp) REVERT: N 244 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8480 (m) REVERT: O 267 MET cc_start: 0.8108 (tmm) cc_final: 0.7883 (tmm) REVERT: O 375 ARG cc_start: 0.6603 (mmt180) cc_final: 0.6053 (tpp80) REVERT: P 68 GLU cc_start: 0.7426 (pp20) cc_final: 0.7006 (pp20) REVERT: Q 109 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.5319 (t80) REVERT: R 58 GLU cc_start: 0.7974 (mp0) cc_final: 0.7737 (mp0) REVERT: S 83 LYS cc_start: 0.5842 (tppp) cc_final: 0.5170 (tttt) REVERT: T 50 GLN cc_start: 0.7973 (mt0) cc_final: 0.7430 (mp10) outliers start: 99 outliers final: 73 residues processed: 456 average time/residue: 0.1706 time to fit residues: 127.8996 Evaluate side-chains 464 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 384 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 317 HIS Chi-restraints excluded: chain M residue 324 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 512 PHE Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 244 THR Chi-restraints excluded: chain N residue 246 LEU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain N residue 468 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain O residue 333 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain P residue 264 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain Q residue 207 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 39 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 301 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 342 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 306 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS N 136 ASN N 140 HIS V 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.181627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.142010 restraints weight = 45229.894| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.28 r_work: 0.3516 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.448 35349 Z= 0.144 Angle : 0.608 21.726 47951 Z= 0.298 Chirality : 0.042 0.184 5134 Planarity : 0.005 0.065 6069 Dihedral : 12.300 112.203 5512 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.82 % Allowed : 16.83 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.21 (0.13), residues: 4181 helix: 1.50 (0.11), residues: 2134 sheet: -0.44 (0.28), residues: 364 loop : -1.56 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 120 TYR 0.011 0.001 TYR D 200 PHE 0.020 0.001 PHE A 318 TRP 0.018 0.001 TRP O 146 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00262 (35325) covalent geometry : angle 0.58947 (47929) SS BOND : bond 0.00193 ( 8) SS BOND : angle 1.89966 ( 16) hydrogen bonds : bond 0.04795 ( 1720) hydrogen bonds : angle 4.02437 ( 4995) metal coordination : bond 0.14226 ( 10) metal coordination : angle 12.84671 ( 6) Misc. bond : bond 0.09163 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 417 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7734 (tp30) cc_final: 0.6755 (mt-10) REVERT: A 318 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.6834 (p90) REVERT: B 392 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8020 (ppp) REVERT: C 6 PHE cc_start: 0.8153 (m-80) cc_final: 0.7848 (m-80) REVERT: H 78 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: J 39 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5786 (tt0) REVERT: M 159 GLU cc_start: 0.7892 (tp30) cc_final: 0.7587 (tp30) REVERT: M 286 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7039 (m) REVERT: M 318 PHE cc_start: 0.8170 (p90) cc_final: 0.7414 (p90) REVERT: M 359 MET cc_start: 0.7007 (ttp) cc_final: 0.5907 (mmt) REVERT: M 471 VAL cc_start: 0.7773 (t) cc_final: 0.7507 (p) REVERT: N 330 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6857 (p0) REVERT: N 392 MET cc_start: 0.8547 (ttp) cc_final: 0.8203 (tmm) REVERT: O 267 MET cc_start: 0.7982 (tmm) cc_final: 0.7631 (tmm) REVERT: O 375 ARG cc_start: 0.6475 (mmt180) cc_final: 0.5922 (tpp80) REVERT: P 68 GLU cc_start: 0.7433 (pp20) cc_final: 0.6345 (tm-30) REVERT: P 116 ASP cc_start: 0.8022 (m-30) cc_final: 0.7547 (t0) REVERT: Q 109 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.4973 (t80) REVERT: S 83 LYS cc_start: 0.5840 (tppp) cc_final: 0.5155 (tttt) REVERT: V 61 ASP cc_start: 0.8644 (m-30) cc_final: 0.8425 (m-30) outliers start: 65 outliers final: 34 residues processed: 456 average time/residue: 0.1791 time to fit residues: 132.5105 Evaluate side-chains 436 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 HIS Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 39 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 320 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 143 optimal weight: 0.0030 chunk 260 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 242 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138810 restraints weight = 45225.134| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.47 r_work: 0.3456 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 35349 Z= 0.157 Angle : 0.646 22.830 47951 Z= 0.316 Chirality : 0.044 0.277 5134 Planarity : 0.005 0.066 6069 Dihedral : 12.248 111.537 5512 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.96 % Allowed : 16.94 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.20 (0.13), residues: 4181 helix: 1.46 (0.11), residues: 2140 sheet: -0.33 (0.29), residues: 330 loop : -1.54 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 120 TYR 0.020 0.001 TYR N 500 PHE 0.025 0.001 PHE O 312 TRP 0.016 0.001 TRP D 274 HIS 0.007 0.001 HIS O 201 Details of bonding type rmsd covalent geometry : bond 0.00373 (35325) covalent geometry : angle 0.62815 (47929) SS BOND : bond 0.00204 ( 8) SS BOND : angle 1.81758 ( 16) hydrogen bonds : bond 0.05831 ( 1720) hydrogen bonds : angle 4.05953 ( 4995) metal coordination : bond 0.01562 ( 10) metal coordination : angle 13.15161 ( 6) Misc. bond : bond 0.11279 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 387 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8231 (mp) cc_final: 0.8021 (mp) REVERT: A 318 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.6851 (p90) REVERT: B 324 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: B 331 GLU cc_start: 0.6851 (mp0) cc_final: 0.6507 (mp0) REVERT: C 6 PHE cc_start: 0.8208 (m-80) cc_final: 0.7991 (m-80) REVERT: H 78 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: J 39 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5701 (tt0) REVERT: M 286 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.6984 (m) REVERT: M 324 LEU cc_start: 0.8015 (tp) cc_final: 0.7777 (mm) REVERT: M 359 MET cc_start: 0.6995 (ttp) cc_final: 0.5866 (mmt) REVERT: N 330 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.6845 (p0) REVERT: O 267 MET cc_start: 0.8021 (tmm) cc_final: 0.7806 (tmm) REVERT: O 375 ARG cc_start: 0.6540 (mmt180) cc_final: 0.5913 (tpp80) REVERT: P 68 GLU cc_start: 0.7469 (pp20) cc_final: 0.6485 (tm-30) REVERT: P 116 ASP cc_start: 0.8103 (m-30) cc_final: 0.7590 (t0) REVERT: Q 109 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.5045 (t80) REVERT: S 83 LYS cc_start: 0.5835 (tppp) cc_final: 0.5145 (tttt) REVERT: V 61 ASP cc_start: 0.8652 (m-30) cc_final: 0.8450 (m-30) outliers start: 70 outliers final: 49 residues processed: 431 average time/residue: 0.1804 time to fit residues: 127.7101 Evaluate side-chains 439 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 383 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 HIS Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 278 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 186 optimal weight: 0.1980 chunk 154 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 332 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 376 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.180135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139654 restraints weight = 45097.189| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.35 r_work: 0.3480 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 35349 Z= 0.135 Angle : 0.618 21.700 47951 Z= 0.302 Chirality : 0.043 0.270 5134 Planarity : 0.005 0.065 6069 Dihedral : 12.022 109.631 5512 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.02 % Allowed : 17.14 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.30 (0.13), residues: 4181 helix: 1.53 (0.11), residues: 2141 sheet: -0.25 (0.29), residues: 330 loop : -1.48 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 120 TYR 0.020 0.001 TYR N 500 PHE 0.020 0.001 PHE A 318 TRP 0.016 0.001 TRP T 74 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00313 (35325) covalent geometry : angle 0.60051 (47929) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.71244 ( 16) hydrogen bonds : bond 0.05361 ( 1720) hydrogen bonds : angle 4.00025 ( 4995) metal coordination : bond 0.01433 ( 10) metal coordination : angle 12.67556 ( 6) Misc. bond : bond 0.10614 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 402 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7749 (tp30) cc_final: 0.6708 (mt-10) REVERT: A 239 LEU cc_start: 0.8246 (mp) cc_final: 0.7948 (mp) REVERT: A 318 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7114 (p90) REVERT: B 324 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: B 331 GLU cc_start: 0.6800 (mp0) cc_final: 0.6437 (mp0) REVERT: C 6 PHE cc_start: 0.8185 (m-80) cc_final: 0.7959 (m-80) REVERT: D 226 MET cc_start: 0.7989 (ttp) cc_final: 0.7037 (ttm) REVERT: H 78 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: J 39 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5913 (tt0) REVERT: M 286 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7022 (m) REVERT: M 324 LEU cc_start: 0.8044 (tp) cc_final: 0.7779 (mm) REVERT: M 359 MET cc_start: 0.6930 (ttp) cc_final: 0.5690 (mmt) REVERT: M 512 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6815 (t80) REVERT: N 148 LYS cc_start: 0.6053 (mmtt) cc_final: 0.5575 (mmtm) REVERT: N 330 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6824 (p0) REVERT: O 267 MET cc_start: 0.8012 (tmm) cc_final: 0.7805 (tmm) REVERT: O 375 ARG cc_start: 0.6558 (mmt180) cc_final: 0.5913 (tpp80) REVERT: O 378 ARG cc_start: 0.7288 (mpt180) cc_final: 0.7062 (mpt180) REVERT: P 68 GLU cc_start: 0.7446 (pp20) cc_final: 0.6371 (tm-30) REVERT: P 116 ASP cc_start: 0.8106 (m-30) cc_final: 0.7619 (t0) REVERT: Q 109 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.4944 (t80) REVERT: S 23 PHE cc_start: 0.6872 (t80) cc_final: 0.6600 (t80) REVERT: S 83 LYS cc_start: 0.5846 (tppp) cc_final: 0.5140 (tttt) REVERT: V 61 ASP cc_start: 0.8624 (m-30) cc_final: 0.8420 (m-30) outliers start: 72 outliers final: 54 residues processed: 447 average time/residue: 0.1756 time to fit residues: 128.4687 Evaluate side-chains 450 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 388 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 HIS Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 504 ASN Chi-restraints excluded: chain M residue 512 PHE Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 409 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 75 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.175795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134944 restraints weight = 45078.575| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.41 r_work: 0.3408 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 35349 Z= 0.229 Angle : 0.730 23.169 47951 Z= 0.356 Chirality : 0.047 0.271 5134 Planarity : 0.006 0.069 6069 Dihedral : 12.399 110.204 5512 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.94 % Allowed : 17.22 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.00 (0.13), residues: 4181 helix: 1.26 (0.11), residues: 2127 sheet: -0.27 (0.28), residues: 346 loop : -1.61 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 120 TYR 0.026 0.002 TYR O 208 PHE 0.025 0.002 PHE N 320 TRP 0.014 0.002 TRP P 78 HIS 0.011 0.001 HIS O 201 Details of bonding type rmsd covalent geometry : bond 0.00562 (35325) covalent geometry : angle 0.71358 (47929) SS BOND : bond 0.00284 ( 8) SS BOND : angle 1.94582 ( 16) hydrogen bonds : bond 0.07301 ( 1720) hydrogen bonds : angle 4.24229 ( 4995) metal coordination : bond 0.01820 ( 10) metal coordination : angle 13.48685 ( 6) Misc. bond : bond 0.15966 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 392 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7832 (tp30) cc_final: 0.6883 (mt-10) REVERT: A 239 LEU cc_start: 0.8295 (mp) cc_final: 0.7965 (mp) REVERT: A 318 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7096 (p90) REVERT: A 357 LYS cc_start: 0.6838 (pptt) cc_final: 0.6271 (mtpt) REVERT: B 324 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: B 331 GLU cc_start: 0.6805 (mp0) cc_final: 0.6441 (mp0) REVERT: H 78 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: J 39 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: M 286 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7043 (m) REVERT: M 324 LEU cc_start: 0.7991 (tp) cc_final: 0.7771 (mm) REVERT: M 359 MET cc_start: 0.7079 (ttp) cc_final: 0.5690 (mmt) REVERT: M 512 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6821 (t80) REVERT: O 267 MET cc_start: 0.8076 (tmm) cc_final: 0.7843 (tmm) REVERT: O 375 ARG cc_start: 0.6573 (mmt180) cc_final: 0.5984 (tpp80) REVERT: O 378 ARG cc_start: 0.7411 (mpt180) cc_final: 0.7206 (mpt180) REVERT: P 68 GLU cc_start: 0.7471 (pp20) cc_final: 0.6492 (tm-30) REVERT: P 116 ASP cc_start: 0.8144 (m-30) cc_final: 0.7620 (t0) REVERT: Q 109 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5132 (t80) REVERT: R 58 GLU cc_start: 0.8079 (mp0) cc_final: 0.7776 (mp0) REVERT: S 83 LYS cc_start: 0.5907 (tppp) cc_final: 0.5228 (tttt) REVERT: V 61 ASP cc_start: 0.8672 (m-30) cc_final: 0.8458 (m-30) outliers start: 69 outliers final: 56 residues processed: 434 average time/residue: 0.1906 time to fit residues: 134.4196 Evaluate side-chains 450 residues out of total 3565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 387 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 78 ASP Chi-restraints excluded: chain J residue 39 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 160 GLN Chi-restraints excluded: chain M residue 164 THR Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 317 HIS Chi-restraints excluded: chain M residue 394 VAL Chi-restraints excluded: chain M residue 504 ASN Chi-restraints excluded: chain M residue 512 PHE Chi-restraints excluded: chain N residue 89 ARG Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 330 ASP Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 450 LEU Chi-restraints excluded: chain N residue 457 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 307 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 209 ILE Chi-restraints excluded: chain P residue 241 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 109 TYR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 39 GLU Chi-restraints excluded: chain V residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 61 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 300 optimal weight: 0.5980 chunk 397 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.178069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138103 restraints weight = 45003.411| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.39 r_work: 0.3444 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 35349 Z= 0.161 Angle : 0.663 21.575 47951 Z= 0.323 Chirality : 0.044 0.257 5134 Planarity : 0.005 0.067 6069 Dihedral : 12.172 108.111 5512 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.82 % Allowed : 17.59 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % 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 aren not related in a simple way. whole: 0.11 (0.13), residues: 4181 helix: 1.37 (0.11), residues: 2132 sheet: -0.20 (0.28), residues: 352 loop : -1.59 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 120 TYR 0.021 0.001 TYR N 500 PHE 0.020 0.001 PHE A 318 TRP 0.015 0.001 TRP T 74 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00383 (35325) covalent geometry : angle 0.64681 (47929) SS BOND : bond 0.00253 ( 8) SS BOND : angle 1.80351 ( 16) hydrogen bonds : bond 0.06124 ( 1720) hydrogen bonds : angle 4.13174 ( 4995) metal coordination : bond 0.01454 ( 10) metal coordination : angle 12.81504 ( 6) Misc. bond : bond 0.13041 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7761.01 seconds wall clock time: 133 minutes 16.37 seconds (7996.37 seconds total)