Starting phenix.real_space_refine on Mon Aug 25 13:20:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpq_18559/08_2025/8qpq_18559.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 Zn 3 6.06 5 P 6 5.49 5 Mg 50 5.21 5 S 60 5.16 5 C 17214 2.51 5 N 4892 2.21 5 O 6038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 residue(s): 0.02s 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: 28263 Number of models: 1 Model: "" Number of chains: 30 Chain: "TC" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3176 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain: "TD" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TE" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TF" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TG" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TH" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TI" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NEP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3176 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain: "TB" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3176 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain: "LA" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2298 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain: "LB" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2298 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain: "LF" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2194 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain: "LE" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2298 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain: "LD" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2298 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain: "LC" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2298 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain: "TC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TE" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TF" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TG" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TH" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TI" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "TB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LA" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "LB" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "LF" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "LE" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "LD" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "LC" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.10, per 1000 atoms: 0.22 Number of scatterers: 28263 At special positions: 0 Unit cell: (154.572, 162.769, 153.401, 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 3 29.99 S 60 16.00 P 6 15.00 Mg 50 11.99 O 6038 8.00 N 4892 7.00 C 17214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNTA 501 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 270 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 266 " pdb=" ZNTB 501 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 270 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 266 " pdb=" ZNTC 501 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 270 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 266 " 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 44 sheets defined 27.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'TC' and resid 48 through 52 removed outlier: 4.241A pdb=" N THRTC 51 " --> pdb=" O LEUTC 48 " (cutoff:3.500A) Processing helix chain 'TC' and resid 61 through 63 No H-bonds generated for 'chain 'TC' and resid 61 through 63' Processing helix chain 'TC' and resid 216 through 226 Processing helix chain 'TC' and resid 248 through 257 Processing helix chain 'TC' and resid 277 through 295 Processing helix chain 'TC' and resid 298 through 303 Processing helix chain 'TC' and resid 308 through 311 Processing helix chain 'TC' and resid 313 through 321 Processing helix chain 'TC' and resid 333 through 337 Processing helix chain 'TC' and resid 358 through 372 Processing helix chain 'TC' and resid 385 through 399 Processing helix chain 'TC' and resid 405 through 413 removed outlier: 3.598A pdb=" N GLNTC 413 " --> pdb=" O PHETC 409 " (cutoff:3.500A) Processing helix chain 'TD' and resid 29 through 33 Processing helix chain 'TE' and resid 29 through 33 Processing helix chain 'TF' and resid 29 through 33 Processing helix chain 'TG' and resid 29 through 33 Processing helix chain 'TH' and resid 29 through 33 Processing helix chain 'TI' and resid 29 through 33 Processing helix chain 'TA' and resid 44 through 48 removed outlier: 4.436A pdb=" N GLNTA 47 " --> pdb=" O ASPTA 44 " (cutoff:3.500A) Processing helix chain 'TA' and resid 61 through 63 No H-bonds generated for 'chain 'TA' and resid 61 through 63' Processing helix chain 'TA' and resid 216 through 226 Processing helix chain 'TA' and resid 248 through 258 removed outlier: 3.651A pdb=" N LYSTA 258 " --> pdb=" O ASPTA 254 " (cutoff:3.500A) Processing helix chain 'TA' and resid 277 through 295 Processing helix chain 'TA' and resid 298 through 303 Processing helix chain 'TA' and resid 308 through 311 Processing helix chain 'TA' and resid 313 through 321 Processing helix chain 'TA' and resid 333 through 337 removed outlier: 3.663A pdb=" N ALATA 337 " --> pdb=" O GLUTA 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'TA' and resid 333 through 337' Processing helix chain 'TA' and resid 358 through 372 Processing helix chain 'TA' and resid 385 through 399 Processing helix chain 'TA' and resid 405 through 413 removed outlier: 3.642A pdb=" N GLNTA 413 " --> pdb=" O PHETA 409 " (cutoff:3.500A) Processing helix chain 'TB' and resid 61 through 63 No H-bonds generated for 'chain 'TB' and resid 61 through 63' Processing helix chain 'TB' and resid 216 through 226 Processing helix chain 'TB' and resid 236 through 240 Processing helix chain 'TB' and resid 248 through 258 removed outlier: 3.647A pdb=" N LYSTB 258 " --> pdb=" O ASPTB 254 " (cutoff:3.500A) Processing helix chain 'TB' and resid 277 through 295 Processing helix chain 'TB' and resid 298 through 303 Processing helix chain 'TB' and resid 308 through 311 Processing helix chain 'TB' and resid 313 through 321 Processing helix chain 'TB' and resid 333 through 337 removed outlier: 3.526A pdb=" N ALATB 337 " --> pdb=" O GLUTB 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'TB' and resid 333 through 337' Processing helix chain 'TB' and resid 358 through 372 Processing helix chain 'TB' and resid 385 through 399 Processing helix chain 'TB' and resid 405 through 412 Processing helix chain 'LA' and resid 104 through 109 Processing helix chain 'LA' and resid 130 through 135 Processing helix chain 'LA' and resid 190 through 196 Processing helix chain 'LA' and resid 199 through 228 removed outlier: 3.518A pdb=" N ALALA 228 " --> pdb=" O LEULA 224 " (cutoff:3.500A) Processing helix chain 'LA' and resid 240 through 254 Processing helix chain 'LA' and resid 264 through 274 Processing helix chain 'LA' and resid 274 through 279 Processing helix chain 'LA' and resid 279 through 284 Processing helix chain 'LA' and resid 286 through 292 Processing helix chain 'LA' and resid 293 through 300 Proline residue: LA 296 - end of helix Processing helix chain 'LA' and resid 311 through 315 removed outlier: 3.556A pdb=" N THRLA 314 " --> pdb=" O SERLA 311 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYRLA 315 " --> pdb=" O SERLA 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 311 through 315' Processing helix chain 'LA' and resid 387 through 389 No H-bonds generated for 'chain 'LA' and resid 387 through 389' Processing helix chain 'LB' and resid 104 through 109 Processing helix chain 'LB' and resid 190 through 196 Processing helix chain 'LB' and resid 199 through 228 removed outlier: 3.530A pdb=" N ALALB 228 " --> pdb=" O LEULB 224 " (cutoff:3.500A) Processing helix chain 'LB' and resid 240 through 254 Processing helix chain 'LB' and resid 264 through 274 Processing helix chain 'LB' and resid 274 through 279 Processing helix chain 'LB' and resid 279 through 284 Processing helix chain 'LB' and resid 286 through 292 Processing helix chain 'LB' and resid 293 through 300 Proline residue: LB 296 - end of helix Processing helix chain 'LB' and resid 311 through 315 removed outlier: 3.539A pdb=" N THRLB 314 " --> pdb=" O SERLB 311 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYRLB 315 " --> pdb=" O SERLB 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 311 through 315' Processing helix chain 'LB' and resid 387 through 389 No H-bonds generated for 'chain 'LB' and resid 387 through 389' Processing helix chain 'LF' and resid 130 through 135 Processing helix chain 'LF' and resid 190 through 196 Processing helix chain 'LF' and resid 199 through 228 removed outlier: 3.525A pdb=" N ALALF 228 " --> pdb=" O LEULF 224 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 254 Processing helix chain 'LF' and resid 264 through 274 Processing helix chain 'LF' and resid 274 through 279 Processing helix chain 'LF' and resid 279 through 284 Processing helix chain 'LF' and resid 286 through 292 Processing helix chain 'LF' and resid 293 through 300 Proline residue: LF 296 - end of helix Processing helix chain 'LF' and resid 311 through 315 removed outlier: 4.145A pdb=" N TYRLF 315 " --> pdb=" O SERLF 312 " (cutoff:3.500A) Processing helix chain 'LF' and resid 387 through 389 No H-bonds generated for 'chain 'LF' and resid 387 through 389' Processing helix chain 'LE' and resid 104 through 109 Processing helix chain 'LE' and resid 130 through 135 Processing helix chain 'LE' and resid 190 through 196 Processing helix chain 'LE' and resid 199 through 228 removed outlier: 3.542A pdb=" N ALALE 228 " --> pdb=" O LEULE 224 " (cutoff:3.500A) Processing helix chain 'LE' and resid 240 through 254 Processing helix chain 'LE' and resid 264 through 274 Processing helix chain 'LE' and resid 274 through 279 Processing helix chain 'LE' and resid 279 through 284 Processing helix chain 'LE' and resid 286 through 292 Processing helix chain 'LE' and resid 293 through 300 Proline residue: LE 296 - end of helix Processing helix chain 'LE' and resid 311 through 315 removed outlier: 3.553A pdb=" N THRLE 314 " --> pdb=" O SERLE 311 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYRLE 315 " --> pdb=" O SERLE 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 311 through 315' Processing helix chain 'LE' and resid 344 through 346 No H-bonds generated for 'chain 'LE' and resid 344 through 346' Processing helix chain 'LE' and resid 387 through 390 Processing helix chain 'LD' and resid 104 through 109 Processing helix chain 'LD' and resid 130 through 135 Processing helix chain 'LD' and resid 190 through 196 Processing helix chain 'LD' and resid 199 through 228 removed outlier: 3.532A pdb=" N ALALD 228 " --> pdb=" O LEULD 224 " (cutoff:3.500A) Processing helix chain 'LD' and resid 240 through 254 Processing helix chain 'LD' and resid 264 through 274 Processing helix chain 'LD' and resid 274 through 279 Processing helix chain 'LD' and resid 279 through 284 Processing helix chain 'LD' and resid 286 through 292 Processing helix chain 'LD' and resid 293 through 295 No H-bonds generated for 'chain 'LD' and resid 293 through 295' Processing helix chain 'LD' and resid 300 through 304 removed outlier: 4.253A pdb=" N GLYLD 303 " --> pdb=" O ASPLD 300 " (cutoff:3.500A) Processing helix chain 'LD' and resid 311 through 315 removed outlier: 3.536A pdb=" N THRLD 314 " --> pdb=" O SERLD 311 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYRLD 315 " --> pdb=" O SERLD 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 311 through 315' Processing helix chain 'LD' and resid 387 through 389 No H-bonds generated for 'chain 'LD' and resid 387 through 389' Processing helix chain 'LC' and resid 104 through 109 removed outlier: 3.700A pdb=" N TYRLC 108 " --> pdb=" O SERLC 104 " (cutoff:3.500A) Processing helix chain 'LC' and resid 130 through 135 Processing helix chain 'LC' and resid 190 through 196 Processing helix chain 'LC' and resid 199 through 228 removed outlier: 3.529A pdb=" N ALALC 228 " --> pdb=" O LEULC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 240 through 254 Processing helix chain 'LC' and resid 264 through 274 Processing helix chain 'LC' and resid 274 through 279 Processing helix chain 'LC' and resid 279 through 284 Processing helix chain 'LC' and resid 286 through 292 Processing helix chain 'LC' and resid 293 through 300 Proline residue: LC 296 - end of helix Processing helix chain 'LC' and resid 311 through 315 removed outlier: 3.565A pdb=" N THRLC 314 " --> pdb=" O SERLC 311 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYRLC 315 " --> pdb=" O SERLC 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 311 through 315' Processing helix chain 'LC' and resid 387 through 389 No H-bonds generated for 'chain 'LC' and resid 387 through 389' Processing sheet with id=AA1, first strand: chain 'TC' and resid 13 through 14 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'TC' and resid 54 through 57 WARNING: can't find start of bonding for strands! previous: chain 'TC' and resid 54 through 57 current: chain 'TC' and resid 85 through 93 WARNING: can't find start of bonding for strands! previous: chain 'TC' and resid 85 through 93 current: chain 'TC' and resid 157 through 160 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'TC' and resid 65 through 69 removed outlier: 6.539A pdb=" N ASPTC 96 " --> pdb=" O ASNTC 68 " (cutoff:3.500A) removed outlier: 12.406A pdb=" N TYRTC 99 " --> pdb=" O THRTC 181 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N THRTC 181 " --> pdb=" O TYRTC 99 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N PHETC 101 " --> pdb=" O THRTC 179 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N THRTC 179 " --> pdb=" O PHETC 101 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N THRTC 103 " --> pdb=" O THRTC 177 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THRTC 177 " --> pdb=" O THRTC 103 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYRTC 141 " --> pdb=" O GLUTC 166 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLUTC 166 " --> pdb=" O TYRTC 141 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THRTC 143 " --> pdb=" O GLUTC 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'TC' and resid 204 through 211 WARNING: can't find start of bonding for strands! previous: chain 'TC' and resid 261 through 265 current: chain 'TC' and resid 374 through 379 Processing sheet with id=AA5, first strand: chain 'TC' and resid 304 through 306 removed outlier: 3.662A pdb=" N TRPTC 328 " --> pdb=" O TYRTC 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'TD' and resid 3 through 9 removed outlier: 4.301A pdb=" N ASPTE 3 " --> pdb=" O THRTD 4 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASPTF 3 " --> pdb=" O THRTE 4 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASPTG 3 " --> pdb=" O THRTF 4 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASPTH 3 " --> pdb=" O THRTG 4 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASPTI 3 " --> pdb=" O THRTH 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASPTD 3 " --> pdb=" O THRTI 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'TD' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TD' and resid 12 through 20 current: chain 'TD' and resid 78 through 79 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'TD' and resid 25 through 28 removed outlier: 3.547A pdb=" N ASPTD 71 " --> pdb=" O VALTD 51 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEUTD 53 " --> pdb=" O THRTD 69 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THRTD 69 " --> pdb=" O LEUTD 53 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THRTD 55 " --> pdb=" O ALATD 67 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALATD 67 " --> pdb=" O THRTD 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'TE' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TE' and resid 12 through 20 current: chain 'TE' and resid 78 through 79 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'TE' and resid 25 through 28 removed outlier: 3.560A pdb=" N ASPTE 71 " --> pdb=" O VALTE 51 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEUTE 53 " --> pdb=" O THRTE 69 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THRTE 69 " --> pdb=" O LEUTE 53 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THRTE 55 " --> pdb=" O ALATE 67 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALATE 67 " --> pdb=" O THRTE 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'TF' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TF' and resid 12 through 20 current: chain 'TF' and resid 78 through 79 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'TF' and resid 25 through 28 removed outlier: 3.556A pdb=" N ASPTF 71 " --> pdb=" O VALTF 51 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEUTF 53 " --> pdb=" O THRTF 69 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THRTF 69 " --> pdb=" O LEUTF 53 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THRTF 55 " --> pdb=" O ALATF 67 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALATF 67 " --> pdb=" O THRTF 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'TG' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TG' and resid 12 through 20 current: chain 'TG' and resid 78 through 79 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'TG' and resid 25 through 28 removed outlier: 3.544A pdb=" N ASPTG 71 " --> pdb=" O VALTG 51 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEUTG 53 " --> pdb=" O THRTG 69 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THRTG 69 " --> pdb=" O LEUTG 53 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THRTG 55 " --> pdb=" O ALATG 67 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALATG 67 " --> pdb=" O THRTG 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'TH' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TH' and resid 12 through 20 current: chain 'TH' and resid 78 through 79 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'TH' and resid 25 through 28 removed outlier: 6.967A pdb=" N VALTH 49 " --> pdb=" O ASPTH 71 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASPTH 71 " --> pdb=" O VALTH 49 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VALTH 51 " --> pdb=" O THRTH 69 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THRTH 69 " --> pdb=" O VALTH 51 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEUTH 53 " --> pdb=" O ALATH 67 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALATH 67 " --> pdb=" O LEUTH 53 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THRTH 55 " --> pdb=" O ASPTH 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'TI' and resid 12 through 20 WARNING: can't find start of bonding for strands! previous: chain 'TI' and resid 12 through 20 current: chain 'TI' and resid 78 through 79 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'TI' and resid 25 through 28 removed outlier: 3.580A pdb=" N ASPTI 71 " --> pdb=" O VALTI 51 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEUTI 53 " --> pdb=" O THRTI 69 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THRTI 69 " --> pdb=" O LEUTI 53 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THRTI 55 " --> pdb=" O ALATI 67 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALATI 67 " --> pdb=" O THRTI 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'TA' and resid 54 through 57 WARNING: can't find start of bonding for strands! previous: chain 'TA' and resid 54 through 57 current: chain 'TA' and resid 85 through 93 WARNING: can't find start of bonding for strands! previous: chain 'TA' and resid 85 through 93 current: chain 'TA' and resid 157 through 160 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'TA' and resid 65 through 69 removed outlier: 6.507A pdb=" N ASPTA 96 " --> pdb=" O ASNTA 68 " (cutoff:3.500A) removed outlier: 12.525A pdb=" N TYRTA 99 " --> pdb=" O THRTA 181 " (cutoff:3.500A) removed outlier: 11.460A pdb=" N THRTA 181 " --> pdb=" O TYRTA 99 " (cutoff:3.500A) removed outlier: 11.251A pdb=" N PHETA 101 " --> pdb=" O THRTA 179 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N THRTA 179 " --> pdb=" O PHETA 101 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THRTA 103 " --> pdb=" O THRTA 177 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THRTA 177 " --> pdb=" O THRTA 103 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SERTA 145 " --> pdb=" O PHETA 163 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHETA 163 " --> pdb=" O SERTA 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'TA' and resid 204 through 211 WARNING: can't find start of bonding for strands! previous: chain 'TA' and resid 261 through 265 current: chain 'TA' and resid 374 through 379 Processing sheet with id=AC4, first strand: chain 'TA' and resid 304 through 306 removed outlier: 3.643A pdb=" N TRPTA 328 " --> pdb=" O TYRTA 305 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'TB' and resid 54 through 57 WARNING: can't find start of bonding for strands! previous: chain 'TB' and resid 54 through 57 current: chain 'TB' and resid 85 through 93 WARNING: can't find start of bonding for strands! previous: chain 'TB' and resid 85 through 93 current: chain 'TB' and resid 157 through 160 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'TB' and resid 65 through 69 removed outlier: 6.497A pdb=" N ASPTB 96 " --> pdb=" O ASNTB 68 " (cutoff:3.500A) removed outlier: 12.556A pdb=" N TYRTB 99 " --> pdb=" O THRTB 181 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N THRTB 181 " --> pdb=" O TYRTB 99 " (cutoff:3.500A) removed outlier: 11.839A pdb=" N PHETB 101 " --> pdb=" O THRTB 179 " (cutoff:3.500A) removed outlier: 11.839A pdb=" N THRTB 179 " --> pdb=" O PHETB 101 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N THRTB 103 " --> pdb=" O THRTB 177 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THRTB 177 " --> pdb=" O THRTB 103 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SERTB 145 " --> pdb=" O PHETB 163 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHETB 163 " --> pdb=" O SERTB 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'TB' and resid 204 through 211 WARNING: can't find start of bonding for strands! previous: chain 'TB' and resid 261 through 265 current: chain 'TB' and resid 374 through 379 Processing sheet with id=AC8, first strand: chain 'TB' and resid 304 through 306 removed outlier: 3.675A pdb=" N TRPTB 328 " --> pdb=" O TYRTB 305 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'LA' and resid 116 through 117 removed outlier: 6.436A pdb=" N GLNLA 116 " --> pdb=" O ASPLB 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LA' and resid 136 through 140 WARNING: can't find start of bonding for strands! previous: chain 'LA' and resid 136 through 140 current: chain 'LA' and resid 372 through 385 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'LA' and resid 144 through 150 Processing sheet with id=AD3, first strand: chain 'LA' and resid 157 through 159 WARNING: can't find start of bonding for strands! previous: chain 'LA' and resid 157 through 159 current: chain 'LF' and resid 372 through 385 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'LA' and resid 230 through 233 WARNING: can't find start of bonding for strands! previous: chain 'LA' and resid 230 through 233 current: chain 'LA' and resid 306 through 309 WARNING: can't find start of bonding for strands! previous: chain 'LA' and resid 306 through 309 current: chain 'LA' and resid 337 through 343 removed outlier: 3.812A pdb=" N ALALA 340 " --> pdb=" O VALLA 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'LB' and resid 116 through 117 removed outlier: 6.238A pdb=" N GLNLB 116 " --> pdb=" O ASPLC 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LB' and resid 136 through 139 WARNING: can't find start of bonding for strands! previous: chain 'LB' and resid 136 through 139 current: chain 'LB' and resid 372 through 385 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'LB' and resid 230 through 233 removed outlier: 3.819A pdb=" N ALALB 340 " --> pdb=" O VALLB 394 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYRLB 261 " --> pdb=" O ALALB 308 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LF' and resid 172 through 178 removed outlier: 3.774A pdb=" N GLNLE 116 " --> pdb=" O VALLF 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'LF' and resid 157 through 159 WARNING: can't find start of bonding for strands! previous: chain 'LF' and resid 157 through 159 current: chain 'LE' and resid 372 through 385 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'LF' and resid 230 through 233 removed outlier: 6.991A pdb=" N ASNLF 230 " --> pdb=" O THRLF 393 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLNLF 395 " --> pdb=" O ASNLF 230 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HISLF 232 " --> pdb=" O GLNLF 395 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALALF 340 " --> pdb=" O VALLF 394 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYRLF 261 " --> pdb=" O ALALF 308 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LE' and resid 172 through 178 Processing sheet with id=AE3, first strand: chain 'LE' and resid 157 through 159 WARNING: can't find start of bonding for strands! previous: chain 'LE' and resid 157 through 159 current: chain 'LD' and resid 372 through 385 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'LE' and resid 230 through 233 removed outlier: 6.919A pdb=" N ASNLE 230 " --> pdb=" O THRLE 393 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLNLE 395 " --> pdb=" O ASNLE 230 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HISLE 232 " --> pdb=" O GLNLE 395 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALALE 340 " --> pdb=" O VALLE 394 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYRLE 261 " --> pdb=" O ALALE 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'LD' and resid 172 through 178 Processing sheet with id=AE6, first strand: chain 'LD' and resid 157 through 159 WARNING: can't find start of bonding for strands! previous: chain 'LD' and resid 157 through 159 current: chain 'LC' and resid 372 through 385 No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'LD' and resid 230 through 233 WARNING: can't find start of bonding for strands! previous: chain 'LD' and resid 230 through 233 current: chain 'LD' and resid 306 through 309 WARNING: can't find start of bonding for strands! previous: chain 'LD' and resid 306 through 309 current: chain 'LD' and resid 337 through 343 removed outlier: 3.850A pdb=" N ALALD 340 " --> pdb=" O VALLD 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LC' and resid 230 through 233 removed outlier: 6.997A pdb=" N ASNLC 230 " --> pdb=" O THRLC 393 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLNLC 395 " --> pdb=" O ASNLC 230 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HISLC 232 " --> pdb=" O GLNLC 395 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALALC 340 " --> pdb=" O VALLC 394 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYRLC 261 " --> pdb=" O ALALC 308 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2304 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: 4.34 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5834 1.32 - 1.45: 7334 1.45 - 1.58: 15374 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 28656 Sorted by residual: bond pdb=" C ARGLC 292 " pdb=" O ARGLC 292 " ideal model delta sigma weight residual 1.243 1.195 0.048 9.50e-03 1.11e+04 2.60e+01 bond pdb=" NE2 NEPTG 45 " pdb=" P NEPTG 45 " ideal model delta sigma weight residual 1.850 1.752 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" NE2 NEPTE 45 " pdb=" P NEPTE 45 " ideal model delta sigma weight residual 1.850 1.754 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" NE2 NEPTI 45 " pdb=" P NEPTI 45 " ideal model delta sigma weight residual 1.850 1.757 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" NE2 NEPTH 45 " pdb=" P NEPTH 45 " ideal model delta sigma weight residual 1.850 1.766 0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 28651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 35672 2.76 - 5.52: 3069 5.52 - 8.29: 220 8.29 - 11.05: 24 11.05 - 13.81: 4 Bond angle restraints: 38989 Sorted by residual: angle pdb=" CA ASPLD 335 " pdb=" CB ASPLD 335 " pdb=" CG ASPLD 335 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.08e+01 angle pdb=" CA ASPLA 335 " pdb=" CB ASPLA 335 " pdb=" CG ASPLA 335 " ideal model delta sigma weight residual 112.60 119.48 -6.88 1.00e+00 1.00e+00 4.73e+01 angle pdb=" CA ASPLD 300 " pdb=" CB ASPLD 300 " pdb=" CG ASPLD 300 " ideal model delta sigma weight residual 112.60 119.38 -6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" CA HISTA 266 " pdb=" CB HISTA 266 " pdb=" CG HISTA 266 " ideal model delta sigma weight residual 113.80 120.56 -6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" CA ASPLF 335 " pdb=" CB ASPLF 335 " pdb=" CG ASPLF 335 " ideal model delta sigma weight residual 112.60 119.32 -6.72 1.00e+00 1.00e+00 4.52e+01 ... (remaining 38984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 15464 17.49 - 34.98: 1185 34.98 - 52.47: 189 52.47 - 69.96: 110 69.96 - 87.45: 43 Dihedral angle restraints: 16991 sinusoidal: 6450 harmonic: 10541 Sorted by residual: dihedral pdb=" CA ILELF 369 " pdb=" C ILELF 369 " pdb=" N ARGLF 370 " pdb=" CA ARGLF 370 " ideal model delta harmonic sigma weight residual -180.00 -144.92 -35.08 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" C ARGLC 290 " pdb=" N ARGLC 290 " pdb=" CA ARGLC 290 " pdb=" CB ARGLC 290 " ideal model delta harmonic sigma weight residual -122.60 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 dihedral pdb=" C ASPLC 105 " pdb=" N ASPLC 105 " pdb=" CA ASPLC 105 " pdb=" CB ASPLC 105 " ideal model delta harmonic sigma weight residual -122.60 -139.64 17.04 0 2.50e+00 1.60e-01 4.65e+01 ... (remaining 16988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3455 0.144 - 0.288: 827 0.288 - 0.431: 83 0.431 - 0.575: 18 0.575 - 0.719: 2 Chirality restraints: 4385 Sorted by residual: chirality pdb=" CA ARGLC 290 " pdb=" N ARGLC 290 " pdb=" C ARGLC 290 " pdb=" CB ARGLC 290 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA ASPLC 105 " pdb=" N ASPLC 105 " pdb=" C ASPLC 105 " pdb=" CB ASPLC 105 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CB VALLF 262 " pdb=" CA VALLF 262 " pdb=" CG1 VALLF 262 " pdb=" CG2 VALLF 262 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.87e+00 ... (remaining 4382 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB NEPTD 45 " 0.098 2.00e-02 2.50e+03 6.26e-02 6.85e+01 pdb=" CG NEPTD 45 " -0.071 2.00e-02 2.50e+03 pdb=" ND1 NEPTD 45 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 NEPTD 45 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 NEPTD 45 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 NEPTD 45 " -0.034 2.00e-02 2.50e+03 pdb=" P NEPTD 45 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB NEPTF 45 " 0.093 2.00e-02 2.50e+03 6.00e-02 6.30e+01 pdb=" CG NEPTF 45 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 NEPTF 45 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 NEPTF 45 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 NEPTF 45 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 NEPTF 45 " -0.032 2.00e-02 2.50e+03 pdb=" P NEPTF 45 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRTC 305 " -0.103 2.00e-02 2.50e+03 5.57e-02 6.20e+01 pdb=" CG TYRTC 305 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYRTC 305 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYRTC 305 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYRTC 305 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYRTC 305 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYRTC 305 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYRTC 305 " -0.077 2.00e-02 2.50e+03 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 171 2.40 - 3.03: 16271 3.03 - 3.65: 44668 3.65 - 4.28: 73473 4.28 - 4.90: 119079 Nonbonded interactions: 253662 Sorted by model distance: nonbonded pdb=" OD2 ASPTA 212 " pdb="ZN ZNTA 501 " model vdw 1.777 2.230 nonbonded pdb=" OD2 ASPTC 212 " pdb="ZN ZNTC 501 " model vdw 1.791 2.230 nonbonded pdb=" OD2 ASPTB 212 " pdb="ZN ZNTB 501 " model vdw 1.807 2.230 nonbonded pdb=" OD1 ASPTB 212 " pdb="ZN ZNTB 501 " model vdw 1.841 2.230 nonbonded pdb=" OD1 ASPTC 212 " pdb="ZN ZNTC 501 " model vdw 1.879 2.230 ... (remaining 253657 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 'LA' and resid 114 through 405) selection = (chain 'LB' and resid 114 through 405) selection = (chain 'LC' and resid 114 through 405) selection = (chain 'LD' and resid 114 through 405) selection = (chain 'LE' and resid 114 through 405) selection = chain 'LF' } ncs_group { reference = chain 'TA' selection = chain 'TB' selection = chain 'TC' } ncs_group { reference = chain 'TD' selection = chain 'TE' selection = chain 'TF' selection = chain 'TG' selection = chain 'TH' selection = chain 'TI' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.560 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 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 0.438 28662 Z= 0.646 Angle : 1.598 13.812 38989 Z= 1.032 Chirality : 0.121 0.719 4385 Planarity : 0.011 0.088 5287 Dihedral : 14.739 87.448 10249 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.82 % Allowed : 4.21 % Favored : 94.97 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.65 (0.12), residues: 3635 helix: -0.37 (0.16), residues: 738 sheet: 0.62 (0.16), residues: 979 loop : -1.00 (0.12), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARGLC 389 TYR 0.105 0.016 TYRLE 267 PHE 0.057 0.010 PHETB 354 TRP 0.077 0.018 TRPTA 156 HIS 0.046 0.005 HISLB 349 Details of bonding type rmsd covalent geometry : bond 0.00933 (28656) covalent geometry : angle 1.59799 (38989) hydrogen bonds : bond 0.14483 ( 820) hydrogen bonds : angle 7.30501 ( 2304) metal coordination : bond 0.41573 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 917 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8751 (t0) cc_final: 0.8470 (t0) REVERT: TC 22 SER cc_start: 0.9240 (t) cc_final: 0.8999 (m) REVERT: TC 65 TRP cc_start: 0.7797 (m100) cc_final: 0.7580 (m-90) REVERT: TC 142 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8559 (ttm-80) REVERT: TC 190 ILE cc_start: 0.8755 (pt) cc_final: 0.8424 (mp) REVERT: TC 194 ASP cc_start: 0.7717 (t0) cc_final: 0.7259 (t0) REVERT: TC 224 PHE cc_start: 0.9273 (m-80) cc_final: 0.9069 (m-80) REVERT: TC 251 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9107 (mt-10) REVERT: TC 362 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8454 (mp0) REVERT: TC 407 MET cc_start: 0.9336 (mpp) cc_final: 0.8781 (mpt) REVERT: TC 411 ASN cc_start: 0.9451 (m-40) cc_final: 0.9119 (m-40) REVERT: TD 39 GLU cc_start: 0.8703 (tt0) cc_final: 0.8362 (tt0) REVERT: TD 58 ASP cc_start: 0.8783 (t70) cc_final: 0.8569 (t0) REVERT: TD 83 GLN cc_start: 0.9073 (mt0) cc_final: 0.8672 (mt0) REVERT: TD 85 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8446 (mt-10) REVERT: TD 88 ASP cc_start: 0.8210 (t0) cc_final: 0.7883 (t0) REVERT: TD 92 THR cc_start: 0.9450 (m) cc_final: 0.9208 (p) REVERT: TD 112 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8569 (mt-10) REVERT: TE 9 GLN cc_start: 0.9374 (tp40) cc_final: 0.9165 (tp40) REVERT: TE 39 GLU cc_start: 0.8779 (tt0) cc_final: 0.8541 (tt0) REVERT: TE 58 ASP cc_start: 0.8716 (t70) cc_final: 0.8471 (t70) REVERT: TE 85 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8715 (mt-10) REVERT: TF 7 ASN cc_start: 0.8958 (m-40) cc_final: 0.8635 (m110) REVERT: TF 39 GLU cc_start: 0.8619 (tt0) cc_final: 0.8171 (tt0) REVERT: TF 83 GLN cc_start: 0.9024 (mt0) cc_final: 0.8804 (tt0) REVERT: TF 92 THR cc_start: 0.9491 (m) cc_final: 0.9190 (p) REVERT: TG 58 ASP cc_start: 0.9056 (t70) cc_final: 0.8719 (t0) REVERT: TG 71 ASP cc_start: 0.9148 (t0) cc_final: 0.8871 (t0) REVERT: TG 83 GLN cc_start: 0.8834 (mt0) cc_final: 0.8630 (mt0) REVERT: TG 92 THR cc_start: 0.9510 (m) cc_final: 0.9306 (p) REVERT: TG 93 TYR cc_start: 0.8837 (m-80) cc_final: 0.8541 (m-80) REVERT: TG 105 ASP cc_start: 0.8866 (m-30) cc_final: 0.8504 (m-30) REVERT: TH 39 GLU cc_start: 0.8748 (tt0) cc_final: 0.8431 (tt0) REVERT: TH 83 GLN cc_start: 0.8904 (mt0) cc_final: 0.8684 (mt0) REVERT: TH 85 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8812 (mt-10) REVERT: TH 93 TYR cc_start: 0.8902 (m-80) cc_final: 0.8650 (m-80) REVERT: TI 7 ASN cc_start: 0.8932 (m-40) cc_final: 0.8567 (m110) REVERT: TI 31 GLN cc_start: 0.8922 (mt0) cc_final: 0.8702 (mt0) REVERT: TA 81 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8381 (m) REVERT: TA 101 PHE cc_start: 0.8528 (m-80) cc_final: 0.8310 (m-80) REVERT: TA 117 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7973 (ttpt) REVERT: TA 194 ASP cc_start: 0.8251 (t70) cc_final: 0.7267 (t0) REVERT: TA 251 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8833 (mt-10) REVERT: TA 360 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8619 (mm-30) REVERT: TA 363 GLN cc_start: 0.9109 (tp40) cc_final: 0.8779 (tp40) REVERT: TA 366 ASN cc_start: 0.9374 (m-40) cc_final: 0.9127 (m110) REVERT: TA 367 ASP cc_start: 0.9276 (m-30) cc_final: 0.8916 (p0) REVERT: TA 371 TYR cc_start: 0.8769 (m-80) cc_final: 0.8431 (m-80) REVERT: TA 372 ASN cc_start: 0.9254 (m-40) cc_final: 0.8941 (m110) REVERT: TA 389 MET cc_start: 0.9291 (mtt) cc_final: 0.8821 (mtm) REVERT: TB 22 SER cc_start: 0.9269 (t) cc_final: 0.9010 (p) REVERT: TB 97 ILE cc_start: 0.9368 (pt) cc_final: 0.9112 (pp) REVERT: TB 171 ASP cc_start: 0.9337 (t0) cc_final: 0.9030 (t0) REVERT: TB 178 MET cc_start: 0.9437 (ptm) cc_final: 0.9206 (ptm) REVERT: TB 222 GLU cc_start: 0.9096 (tt0) cc_final: 0.8654 (tm-30) REVERT: TB 238 LYS cc_start: 0.9428 (tttt) cc_final: 0.9107 (ttpp) REVERT: TB 247 LEU cc_start: 0.9356 (mt) cc_final: 0.9149 (mp) REVERT: TB 254 ASP cc_start: 0.9379 (m-30) cc_final: 0.9138 (m-30) REVERT: TB 272 ASP cc_start: 0.8666 (p0) cc_final: 0.7958 (p0) REVERT: TB 319 MET cc_start: 0.9347 (tmm) cc_final: 0.9105 (tmt) REVERT: TB 347 TRP cc_start: 0.9247 (m100) cc_final: 0.8868 (m100) REVERT: TB 362 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8454 (mm-30) REVERT: TB 389 MET cc_start: 0.9363 (mtt) cc_final: 0.8990 (mtm) REVERT: TB 394 GLN cc_start: 0.9521 (mt0) cc_final: 0.9238 (mp10) REVERT: LA 120 VAL cc_start: 0.9263 (t) cc_final: 0.9056 (m) REVERT: LA 192 MET cc_start: 0.8890 (tpt) cc_final: 0.7959 (tpp) REVERT: LA 281 ASN cc_start: 0.8719 (t0) cc_final: 0.8482 (t0) REVERT: LA 363 LYS cc_start: 0.9172 (mttt) cc_final: 0.8835 (mtpp) REVERT: LB 126 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8533 (pm20) REVERT: LB 192 MET cc_start: 0.9237 (tpt) cc_final: 0.7946 (mtt) REVERT: LB 275 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8959 (t) REVERT: LB 310 MET cc_start: 0.9329 (mmt) cc_final: 0.9032 (mmt) REVERT: LF 192 MET cc_start: 0.7935 (ttp) cc_final: 0.7190 (mmt) REVERT: LF 195 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8303 (mt0) REVERT: LF 202 GLU cc_start: 0.8943 (tt0) cc_final: 0.8618 (tp30) REVERT: LF 255 ASP cc_start: 0.8434 (m-30) cc_final: 0.8096 (m-30) REVERT: LF 370 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.6466 (tpm-80) REVERT: LE 122 MET cc_start: 0.9266 (mmt) cc_final: 0.8988 (mmt) REVERT: LE 161 GLN cc_start: 0.8744 (tt0) cc_final: 0.8480 (tt0) REVERT: LE 192 MET cc_start: 0.8950 (tpt) cc_final: 0.7621 (mtt) REVERT: LD 120 VAL cc_start: 0.9114 (t) cc_final: 0.8794 (p) REVERT: LD 192 MET cc_start: 0.8166 (ttt) cc_final: 0.7317 (OUTLIER) REVERT: LC 105 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8867 (p0) REVERT: LC 120 VAL cc_start: 0.9249 (t) cc_final: 0.9008 (m) REVERT: LC 192 MET cc_start: 0.8945 (tpt) cc_final: 0.7601 (mtt) REVERT: LC 255 ASP cc_start: 0.8576 (m-30) cc_final: 0.8371 (m-30) outliers start: 25 outliers final: 6 residues processed: 931 average time/residue: 0.5288 time to fit residues: 586.4926 Evaluate side-chains 601 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 593 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TA residue 81 VAL Chi-restraints excluded: chain TB residue 130 ILE Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LB residue 105 ASP Chi-restraints excluded: chain LB residue 262 VAL Chi-restraints excluded: chain LB residue 275 THR Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LC residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 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: TC 47 GLN TC 84 GLN TC 183 ASN TC 205 GLN TC 260 HIS TC 324 HIS TC 349 ASN ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TG 31 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 42 ASN TH 80 GLN TI 83 GLN TA 47 GLN TA 68 ASN TA 140 ASN TA 183 ASN TA 260 HIS ** TA 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TB 47 GLN TB 138 ASN TB 183 ASN ** TB 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TB 303 ASN TB 324 HIS LA 376 ASN LA 395 GLN LB 227 ASN LF 136 ASN LF 206 GLN LF 227 ASN LF 229 GLN ** LF 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 349 HIS LE 136 ASN LE 227 ASN LE 242 GLN LE 376 ASN LD 206 GLN LD 227 ASN LD 349 HIS LC 227 ASN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 349 HIS ** LC 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.065912 restraints weight = 51009.686| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.37 r_work: 0.2620 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 28662 Z= 0.277 Angle : 0.641 8.571 38989 Z= 0.352 Chirality : 0.049 0.295 4385 Planarity : 0.004 0.046 5287 Dihedral : 6.780 59.490 4040 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.58 % Allowed : 12.22 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.13), residues: 3635 helix: 1.17 (0.19), residues: 741 sheet: 0.34 (0.15), residues: 1031 loop : -0.57 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLE 257 TYR 0.028 0.002 TYRTC 290 PHE 0.025 0.002 PHETA 354 TRP 0.023 0.002 TRPLF 177 HIS 0.008 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00614 (28656) covalent geometry : angle 0.64052 (38989) hydrogen bonds : bond 0.04935 ( 820) hydrogen bonds : angle 5.73665 ( 2304) metal coordination : bond 0.00182 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 614 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8696 (t0) cc_final: 0.8393 (t70) REVERT: TC 19 SER cc_start: 0.9073 (t) cc_final: 0.8838 (p) REVERT: TC 22 SER cc_start: 0.9057 (t) cc_final: 0.8677 (m) REVERT: TC 105 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8653 (mm-40) REVERT: TC 131 LYS cc_start: 0.8414 (mppt) cc_final: 0.8201 (mtmt) REVERT: TC 142 ARG cc_start: 0.8703 (ttm170) cc_final: 0.8274 (ttm-80) REVERT: TC 171 ASP cc_start: 0.9309 (t0) cc_final: 0.8611 (p0) REVERT: TC 194 ASP cc_start: 0.7767 (t0) cc_final: 0.6896 (t0) REVERT: TC 251 GLU cc_start: 0.9455 (mt-10) cc_final: 0.8883 (mt-10) REVERT: TC 326 MET cc_start: 0.9175 (ttm) cc_final: 0.8903 (ttm) REVERT: TC 352 CYS cc_start: 0.8662 (t) cc_final: 0.8236 (t) REVERT: TC 407 MET cc_start: 0.9312 (mpp) cc_final: 0.8996 (mpp) REVERT: TC 411 ASN cc_start: 0.9341 (m-40) cc_final: 0.8829 (m-40) REVERT: TD 39 GLU cc_start: 0.8924 (tt0) cc_final: 0.8530 (tt0) REVERT: TD 58 ASP cc_start: 0.8857 (t70) cc_final: 0.8445 (t70) REVERT: TD 83 GLN cc_start: 0.9039 (mt0) cc_final: 0.8449 (tt0) REVERT: TD 85 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8666 (mt-10) REVERT: TD 88 ASP cc_start: 0.8970 (t0) cc_final: 0.8707 (t0) REVERT: TD 92 THR cc_start: 0.9673 (m) cc_final: 0.9317 (p) REVERT: TD 112 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8893 (mt-10) REVERT: TE 9 GLN cc_start: 0.9306 (tp40) cc_final: 0.8965 (tp-100) REVERT: TE 58 ASP cc_start: 0.8871 (t70) cc_final: 0.8293 (t70) REVERT: TE 83 GLN cc_start: 0.9107 (tt0) cc_final: 0.8897 (tt0) REVERT: TE 85 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8938 (mt-10) REVERT: TF 7 ASN cc_start: 0.9101 (m-40) cc_final: 0.8771 (m110) REVERT: TF 39 GLU cc_start: 0.8805 (tt0) cc_final: 0.8134 (tt0) REVERT: TF 83 GLN cc_start: 0.8926 (mt0) cc_final: 0.8500 (tt0) REVERT: TF 92 THR cc_start: 0.9720 (m) cc_final: 0.9038 (p) REVERT: TG 7 ASN cc_start: 0.8960 (m-40) cc_final: 0.8678 (m-40) REVERT: TG 58 ASP cc_start: 0.8979 (t70) cc_final: 0.8428 (t0) REVERT: TG 71 ASP cc_start: 0.9218 (t0) cc_final: 0.8627 (t0) REVERT: TG 83 GLN cc_start: 0.9003 (mt0) cc_final: 0.8672 (tt0) REVERT: TG 92 THR cc_start: 0.9616 (m) cc_final: 0.9249 (p) REVERT: TG 93 TYR cc_start: 0.9195 (m-80) cc_final: 0.8877 (m-80) REVERT: TG 105 ASP cc_start: 0.9135 (m-30) cc_final: 0.8716 (m-30) REVERT: TH 7 ASN cc_start: 0.8770 (m110) cc_final: 0.8522 (m110) REVERT: TH 29 ASP cc_start: 0.9349 (t0) cc_final: 0.9127 (t70) REVERT: TH 39 GLU cc_start: 0.8987 (tt0) cc_final: 0.8676 (tt0) REVERT: TH 58 ASP cc_start: 0.8743 (t70) cc_final: 0.8464 (t0) REVERT: TH 76 GLU cc_start: 0.9035 (tt0) cc_final: 0.8795 (tt0) REVERT: TH 83 GLN cc_start: 0.9037 (mt0) cc_final: 0.8526 (mt0) REVERT: TH 85 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8937 (mt-10) REVERT: TH 92 THR cc_start: 0.9641 (m) cc_final: 0.9362 (p) REVERT: TI 83 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8821 (tt0) REVERT: TI 111 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8954 (mtm-85) REVERT: TA 22 SER cc_start: 0.8960 (t) cc_final: 0.8534 (m) REVERT: TA 141 TYR cc_start: 0.8794 (m-80) cc_final: 0.8555 (m-10) REVERT: TA 194 ASP cc_start: 0.8342 (t70) cc_final: 0.7333 (t0) REVERT: TA 222 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: TA 251 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8823 (mt-10) REVERT: TA 360 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8740 (mm-30) REVERT: TA 366 ASN cc_start: 0.9424 (m-40) cc_final: 0.9189 (m110) REVERT: TA 367 ASP cc_start: 0.9325 (m-30) cc_final: 0.9044 (m-30) REVERT: TA 371 TYR cc_start: 0.8960 (m-80) cc_final: 0.8738 (m-10) REVERT: TA 372 ASN cc_start: 0.9133 (m-40) cc_final: 0.8683 (m-40) REVERT: TA 389 MET cc_start: 0.9227 (mtt) cc_final: 0.8898 (mtm) REVERT: TB 22 SER cc_start: 0.9349 (t) cc_final: 0.8875 (p) REVERT: TB 81 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.7894 (t) REVERT: TB 97 ILE cc_start: 0.9369 (pt) cc_final: 0.8852 (mm) REVERT: TB 98 ARG cc_start: 0.8560 (ptp-170) cc_final: 0.7707 (ptp90) REVERT: TB 120 ASP cc_start: 0.8811 (t0) cc_final: 0.8068 (p0) REVERT: TB 133 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6267 (mtm180) REVERT: TB 138 ASN cc_start: 0.8790 (t160) cc_final: 0.8519 (t0) REVERT: TB 171 ASP cc_start: 0.9385 (t0) cc_final: 0.8610 (p0) REVERT: TB 217 ASP cc_start: 0.9272 (m-30) cc_final: 0.8851 (m-30) REVERT: TB 229 ILE cc_start: 0.9531 (mp) cc_final: 0.9194 (tp) REVERT: TB 247 LEU cc_start: 0.9101 (mt) cc_final: 0.8884 (mt) REVERT: TB 251 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8796 (mt-10) REVERT: TB 272 ASP cc_start: 0.8584 (p0) cc_final: 0.7888 (p0) REVERT: TB 282 GLU cc_start: 0.9314 (tt0) cc_final: 0.9108 (tt0) REVERT: TB 315 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8848 (mp0) REVERT: TB 347 TRP cc_start: 0.9135 (m100) cc_final: 0.8694 (m100) REVERT: TB 362 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8270 (mm-30) REVERT: LA 120 VAL cc_start: 0.9138 (t) cc_final: 0.8916 (m) REVERT: LA 126 GLU cc_start: 0.8384 (pp20) cc_final: 0.8133 (pp20) REVERT: LA 192 MET cc_start: 0.9394 (tpt) cc_final: 0.7988 (tpp) REVERT: LA 202 GLU cc_start: 0.8944 (tt0) cc_final: 0.8556 (tp30) REVERT: LA 281 ASN cc_start: 0.8797 (t0) cc_final: 0.8291 (t0) REVERT: LA 337 ASP cc_start: 0.9137 (m-30) cc_final: 0.8850 (m-30) REVERT: LA 363 LYS cc_start: 0.8960 (mttt) cc_final: 0.8452 (mtpp) REVERT: LA 378 ARG cc_start: 0.9123 (ptp90) cc_final: 0.8803 (ptp-110) REVERT: LA 379 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8862 (tp) REVERT: LB 126 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8224 (pm20) REVERT: LB 192 MET cc_start: 0.9473 (tpt) cc_final: 0.7556 (mtt) REVERT: LB 293 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: LB 363 LYS cc_start: 0.9444 (mttt) cc_final: 0.9230 (mttt) REVERT: LF 133 GLU cc_start: 0.8922 (tp30) cc_final: 0.8597 (mp0) REVERT: LF 192 MET cc_start: 0.7198 (ttp) cc_final: 0.6291 (mmt) REVERT: LF 195 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8052 (mt0) REVERT: LF 202 GLU cc_start: 0.9025 (tt0) cc_final: 0.8377 (tp30) REVERT: LF 206 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8715 (mm110) REVERT: LF 306 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9263 (ttp) REVERT: LF 337 ASP cc_start: 0.9159 (m-30) cc_final: 0.8674 (m-30) REVERT: LF 361 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: LF 370 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.6503 (tpm-80) REVERT: LE 133 GLU cc_start: 0.8274 (mp0) cc_final: 0.7978 (mp0) REVERT: LE 192 MET cc_start: 0.8864 (tpt) cc_final: 0.7252 (mtt) REVERT: LE 287 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8783 (mm-30) REVERT: LE 361 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: LD 101 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7692 (p90) REVERT: LD 105 ASP cc_start: 0.8222 (m-30) cc_final: 0.7726 (t0) REVERT: LD 120 VAL cc_start: 0.9117 (t) cc_final: 0.8746 (p) REVERT: LD 192 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7034 (mtt) REVERT: LD 253 LYS cc_start: 0.9342 (ttpt) cc_final: 0.9006 (ttmt) REVERT: LD 361 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: LC 171 THR cc_start: 0.9050 (m) cc_final: 0.8721 (p) REVERT: LC 192 MET cc_start: 0.9292 (tpt) cc_final: 0.7555 (mtt) REVERT: LC 197 MET cc_start: 0.9113 (mmm) cc_final: 0.8104 (mpt) REVERT: LC 290 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8479 (mtm-85) REVERT: LC 345 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8942 (ttp-170) outliers start: 109 outliers final: 37 residues processed: 687 average time/residue: 0.5641 time to fit residues: 455.6074 Evaluate side-chains 580 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 529 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 50 SER Chi-restraints excluded: chain TC residue 85 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 195 ILE Chi-restraints excluded: chain TC residue 223 VAL Chi-restraints excluded: chain TD residue 26 LEU Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 40 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TA residue 339 THR Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 88 LEU Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 168 THR Chi-restraints excluded: chain TB residue 177 THR Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LB residue 105 ASP Chi-restraints excluded: chain LB residue 120 VAL Chi-restraints excluded: chain LB residue 201 ILE Chi-restraints excluded: chain LB residue 262 VAL Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 117 LEU Chi-restraints excluded: chain LF residue 186 SER Chi-restraints excluded: chain LF residue 306 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LE residue 101 PHE Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 311 SER Chi-restraints excluded: chain LE residue 361 GLU Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 101 PHE Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 301 ILE Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 101 PHE Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 359 ASP Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 278 optimal weight: 2.9990 chunk 212 optimal weight: 0.0000 chunk 23 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 342 GLN TC 349 ASN ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN TE 9 GLN TF 31 GLN TG 31 GLN TI 80 GLN TI 83 GLN TA 324 HIS TB 138 ASN TB 140 ASN ** TB 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN LB 238 ASN LB 270 GLN ** LB 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LF 229 GLN LE 376 ASN LD 136 ASN LD 276 ASN LC 136 ASN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 376 ASN ** LC 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.067543 restraints weight = 50968.206| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.41 r_work: 0.2669 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28662 Z= 0.147 Angle : 0.551 7.560 38989 Z= 0.301 Chirality : 0.046 0.265 4385 Planarity : 0.003 0.042 5287 Dihedral : 6.268 64.727 4034 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.73 % Allowed : 14.43 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.13), residues: 3635 helix: 1.50 (0.19), residues: 736 sheet: 0.27 (0.16), residues: 1036 loop : -0.55 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGLB 193 TYR 0.027 0.002 TYRTC 290 PHE 0.021 0.001 PHETA 354 TRP 0.016 0.002 TRPLB 177 HIS 0.004 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00325 (28656) covalent geometry : angle 0.55076 (38989) hydrogen bonds : bond 0.04072 ( 820) hydrogen bonds : angle 5.41707 ( 2304) metal coordination : bond 0.00137 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 598 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8644 (t0) cc_final: 0.8229 (t70) REVERT: TC 22 SER cc_start: 0.9015 (t) cc_final: 0.8607 (m) REVERT: TC 80 TYR cc_start: 0.9256 (t80) cc_final: 0.9034 (t80) REVERT: TC 114 MET cc_start: 0.8697 (ttp) cc_final: 0.8119 (tmm) REVERT: TC 120 ASP cc_start: 0.8654 (t0) cc_final: 0.8391 (t0) REVERT: TC 131 LYS cc_start: 0.8236 (mppt) cc_final: 0.7914 (mtmt) REVERT: TC 142 ARG cc_start: 0.8745 (ttm170) cc_final: 0.8341 (ttm-80) REVERT: TC 171 ASP cc_start: 0.9313 (t0) cc_final: 0.8573 (p0) REVERT: TC 178 MET cc_start: 0.9448 (ptm) cc_final: 0.9037 (ppp) REVERT: TC 194 ASP cc_start: 0.7737 (t0) cc_final: 0.6965 (t0) REVERT: TC 251 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9010 (mt-10) REVERT: TC 256 LEU cc_start: 0.9482 (mt) cc_final: 0.9269 (mm) REVERT: TC 294 ASP cc_start: 0.8854 (m-30) cc_final: 0.8611 (m-30) REVERT: TC 352 CYS cc_start: 0.8517 (t) cc_final: 0.8010 (t) REVERT: TC 407 MET cc_start: 0.9367 (mpp) cc_final: 0.8995 (mpp) REVERT: TC 411 ASN cc_start: 0.9312 (m-40) cc_final: 0.8854 (m-40) REVERT: TD 39 GLU cc_start: 0.8884 (tt0) cc_final: 0.8534 (tt0) REVERT: TD 58 ASP cc_start: 0.8902 (t70) cc_final: 0.8453 (t0) REVERT: TD 83 GLN cc_start: 0.8979 (mt0) cc_final: 0.8381 (tt0) REVERT: TD 85 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8520 (mt-10) REVERT: TE 9 GLN cc_start: 0.9198 (tp-100) cc_final: 0.8953 (tp-100) REVERT: TE 58 ASP cc_start: 0.8896 (t70) cc_final: 0.8447 (t70) REVERT: TE 83 GLN cc_start: 0.9113 (tt0) cc_final: 0.8792 (tt0) REVERT: TE 85 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8682 (mt-10) REVERT: TF 7 ASN cc_start: 0.9050 (m-40) cc_final: 0.8820 (m110) REVERT: TF 39 GLU cc_start: 0.8870 (tt0) cc_final: 0.8281 (tt0) REVERT: TF 83 GLN cc_start: 0.8799 (mt0) cc_final: 0.8406 (tt0) REVERT: TF 92 THR cc_start: 0.9706 (m) cc_final: 0.9035 (p) REVERT: TG 7 ASN cc_start: 0.8927 (m-40) cc_final: 0.8573 (m-40) REVERT: TG 58 ASP cc_start: 0.9037 (t70) cc_final: 0.8478 (t0) REVERT: TG 71 ASP cc_start: 0.9175 (t0) cc_final: 0.8751 (t0) REVERT: TG 83 GLN cc_start: 0.9050 (mt0) cc_final: 0.8736 (tt0) REVERT: TG 92 THR cc_start: 0.9588 (m) cc_final: 0.9171 (p) REVERT: TG 93 TYR cc_start: 0.9198 (m-80) cc_final: 0.8892 (m-80) REVERT: TH 29 ASP cc_start: 0.9352 (t0) cc_final: 0.9110 (t70) REVERT: TH 39 GLU cc_start: 0.8910 (tt0) cc_final: 0.8627 (tt0) REVERT: TH 58 ASP cc_start: 0.8849 (t70) cc_final: 0.8608 (t70) REVERT: TH 83 GLN cc_start: 0.8963 (mt0) cc_final: 0.8540 (mt0) REVERT: TH 85 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8971 (mt-10) REVERT: TH 92 THR cc_start: 0.9643 (m) cc_final: 0.9264 (p) REVERT: TI 31 GLN cc_start: 0.9188 (mt0) cc_final: 0.8924 (mt0) REVERT: TA 22 SER cc_start: 0.8892 (t) cc_final: 0.8484 (m) REVERT: TA 112 PHE cc_start: 0.8825 (m-80) cc_final: 0.8609 (m-80) REVERT: TA 131 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8510 (mppt) REVERT: TA 141 TYR cc_start: 0.8799 (m-80) cc_final: 0.8597 (m-10) REVERT: TA 194 ASP cc_start: 0.8266 (t70) cc_final: 0.7255 (t0) REVERT: TA 222 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: TA 251 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8830 (mt-10) REVERT: TA 315 GLU cc_start: 0.8769 (mp0) cc_final: 0.8496 (pm20) REVERT: TA 360 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8817 (tp30) REVERT: TA 367 ASP cc_start: 0.9128 (m-30) cc_final: 0.8759 (m-30) REVERT: TA 372 ASN cc_start: 0.9133 (m-40) cc_final: 0.8744 (m-40) REVERT: TA 389 MET cc_start: 0.9161 (mtt) cc_final: 0.8822 (mtm) REVERT: TB 22 SER cc_start: 0.9302 (t) cc_final: 0.8821 (p) REVERT: TB 65 TRP cc_start: 0.8409 (m-90) cc_final: 0.8037 (m-90) REVERT: TB 98 ARG cc_start: 0.8622 (ptp-170) cc_final: 0.8368 (ptp90) REVERT: TB 120 ASP cc_start: 0.8826 (t0) cc_final: 0.8070 (p0) REVERT: TB 131 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7775 (mptt) REVERT: TB 133 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6653 (mtm180) REVERT: TB 138 ASN cc_start: 0.8890 (t0) cc_final: 0.8605 (t0) REVERT: TB 171 ASP cc_start: 0.9392 (t0) cc_final: 0.8587 (p0) REVERT: TB 178 MET cc_start: 0.9216 (ptm) cc_final: 0.8871 (pmm) REVERT: TB 238 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8789 (ttpp) REVERT: TB 251 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8737 (mt-10) REVERT: TB 272 ASP cc_start: 0.8620 (p0) cc_final: 0.7921 (p0) REVERT: TB 283 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8326 (p0) REVERT: TB 347 TRP cc_start: 0.9096 (m100) cc_final: 0.8807 (m100) REVERT: TB 362 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8333 (mm-30) REVERT: LA 120 VAL cc_start: 0.9182 (t) cc_final: 0.8949 (m) REVERT: LA 192 MET cc_start: 0.9394 (tpt) cc_final: 0.7800 (mtt) REVERT: LA 202 GLU cc_start: 0.8958 (tt0) cc_final: 0.8583 (tp30) REVERT: LA 337 ASP cc_start: 0.9100 (m-30) cc_final: 0.8750 (m-30) REVERT: LA 361 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: LA 363 LYS cc_start: 0.8936 (mttt) cc_final: 0.8384 (mtpm) REVERT: LA 378 ARG cc_start: 0.9205 (ptp90) cc_final: 0.8889 (ptp-110) REVERT: LA 379 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8918 (tp) REVERT: LB 126 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8240 (pm20) REVERT: LB 192 MET cc_start: 0.9401 (tpt) cc_final: 0.7446 (mtt) REVERT: LB 293 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: LF 153 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8519 (mt-10) REVERT: LF 192 MET cc_start: 0.6892 (ttp) cc_final: 0.6110 (mmt) REVERT: LF 202 GLU cc_start: 0.9015 (tt0) cc_final: 0.8522 (tm-30) REVERT: LF 206 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8875 (mm110) REVERT: LF 337 ASP cc_start: 0.9096 (m-30) cc_final: 0.8614 (m-30) REVERT: LF 361 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: LF 370 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.6522 (tpm-80) REVERT: LE 133 GLU cc_start: 0.8322 (mp0) cc_final: 0.8035 (mp0) REVERT: LE 192 MET cc_start: 0.8852 (tpt) cc_final: 0.7182 (mtt) REVERT: LE 337 ASP cc_start: 0.9162 (m-30) cc_final: 0.8877 (m-30) REVERT: LD 105 ASP cc_start: 0.8192 (m-30) cc_final: 0.7731 (t0) REVERT: LD 120 VAL cc_start: 0.9191 (t) cc_final: 0.8840 (p) REVERT: LD 192 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: LD 356 ASN cc_start: 0.9350 (m-40) cc_final: 0.9011 (m110) REVERT: LD 361 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: LC 171 THR cc_start: 0.9025 (m) cc_final: 0.8695 (p) REVERT: LC 192 MET cc_start: 0.9209 (tpt) cc_final: 0.7447 (mtt) REVERT: LC 197 MET cc_start: 0.9027 (mmm) cc_final: 0.8142 (mpt) REVERT: LC 290 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8442 (mtm-85) outliers start: 83 outliers final: 28 residues processed: 644 average time/residue: 0.5482 time to fit residues: 415.2323 Evaluate side-chains 565 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 527 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 62 LEU Chi-restraints excluded: chain TC residue 85 SER Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TA residue 339 THR Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain TB residue 283 ASP Chi-restraints excluded: chain TB residue 339 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 361 GLU Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LB residue 121 VAL Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LE residue 105 ASP Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 216 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 105 GLN ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN TG 31 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 80 GLN TI 83 GLN TA 205 GLN TB 205 GLN TB 260 HIS ** TB 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN ** LB 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 349 HIS LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 356 ASN LE 376 ASN LD 136 ASN ** LD 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 347 ASN LC 239 GLN LC 270 GLN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 376 ASN ** LC 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.064213 restraints weight = 51598.824| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.34 r_work: 0.2610 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 28662 Z= 0.324 Angle : 0.622 9.419 38989 Z= 0.335 Chirality : 0.049 0.275 4385 Planarity : 0.004 0.043 5287 Dihedral : 6.113 60.303 4031 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.19 % Allowed : 15.77 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.13), residues: 3635 helix: 1.46 (0.19), residues: 735 sheet: 0.12 (0.15), residues: 1058 loop : -0.64 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGTG 111 TYR 0.027 0.002 TYRTC 290 PHE 0.019 0.002 PHETA 354 TRP 0.018 0.002 TRPLB 177 HIS 0.009 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00720 (28656) covalent geometry : angle 0.62230 (38989) hydrogen bonds : bond 0.04436 ( 820) hydrogen bonds : angle 5.48607 ( 2304) metal coordination : bond 0.00347 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 522 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8553 (t0) cc_final: 0.8348 (t70) REVERT: TC 22 SER cc_start: 0.9090 (t) cc_final: 0.8609 (m) REVERT: TC 120 ASP cc_start: 0.8854 (t0) cc_final: 0.8610 (t0) REVERT: TC 131 LYS cc_start: 0.8292 (mppt) cc_final: 0.8024 (mtmt) REVERT: TC 142 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8475 (ttm-80) REVERT: TC 251 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9042 (mt-10) REVERT: TC 294 ASP cc_start: 0.8913 (m-30) cc_final: 0.8662 (m-30) REVERT: TC 352 CYS cc_start: 0.8688 (t) cc_final: 0.8213 (t) REVERT: TC 372 ASN cc_start: 0.9124 (m-40) cc_final: 0.8090 (p0) REVERT: TC 407 MET cc_start: 0.9362 (mpp) cc_final: 0.8999 (mpp) REVERT: TC 411 ASN cc_start: 0.9315 (m-40) cc_final: 0.8735 (m-40) REVERT: TD 39 GLU cc_start: 0.8933 (tt0) cc_final: 0.8593 (tt0) REVERT: TD 58 ASP cc_start: 0.8939 (t70) cc_final: 0.8445 (t0) REVERT: TD 65 ASP cc_start: 0.8908 (t0) cc_final: 0.8658 (t0) REVERT: TD 83 GLN cc_start: 0.9116 (mt0) cc_final: 0.8609 (tt0) REVERT: TD 85 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8629 (mt-10) REVERT: TE 9 GLN cc_start: 0.9213 (tp-100) cc_final: 0.8901 (tp-100) REVERT: TE 58 ASP cc_start: 0.8905 (t70) cc_final: 0.8434 (t70) REVERT: TE 85 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9084 (mt-10) REVERT: TF 7 ASN cc_start: 0.9105 (m-40) cc_final: 0.8801 (m110) REVERT: TF 39 GLU cc_start: 0.9003 (tt0) cc_final: 0.8453 (tt0) REVERT: TF 83 GLN cc_start: 0.8882 (mt0) cc_final: 0.8484 (tt0) REVERT: TF 92 THR cc_start: 0.9700 (m) cc_final: 0.9078 (p) REVERT: TG 7 ASN cc_start: 0.8942 (m-40) cc_final: 0.8615 (m-40) REVERT: TG 71 ASP cc_start: 0.9136 (t0) cc_final: 0.8597 (t0) REVERT: TG 83 GLN cc_start: 0.9222 (mt0) cc_final: 0.8846 (tt0) REVERT: TG 92 THR cc_start: 0.9572 (m) cc_final: 0.9204 (p) REVERT: TG 93 TYR cc_start: 0.9218 (m-80) cc_final: 0.8923 (m-80) REVERT: TG 105 ASP cc_start: 0.9118 (m-30) cc_final: 0.8617 (m-30) REVERT: TH 58 ASP cc_start: 0.8875 (t70) cc_final: 0.8583 (t70) REVERT: TH 83 GLN cc_start: 0.9033 (mt0) cc_final: 0.8586 (mt0) REVERT: TH 85 GLU cc_start: 0.9422 (mt-10) cc_final: 0.8807 (mt-10) REVERT: TH 92 THR cc_start: 0.9637 (m) cc_final: 0.9358 (p) REVERT: TI 11 SER cc_start: 0.9217 (m) cc_final: 0.8888 (t) REVERT: TA 22 SER cc_start: 0.8932 (t) cc_final: 0.8516 (m) REVERT: TA 112 PHE cc_start: 0.8934 (m-80) cc_final: 0.8731 (m-80) REVERT: TA 131 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8152 (mppt) REVERT: TA 141 TYR cc_start: 0.8826 (m-80) cc_final: 0.8618 (m-10) REVERT: TA 194 ASP cc_start: 0.8326 (t70) cc_final: 0.7351 (t0) REVERT: TA 208 VAL cc_start: 0.9579 (t) cc_final: 0.9379 (p) REVERT: TA 222 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: TA 251 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8774 (mt-10) REVERT: TA 280 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8699 (mt-10) REVERT: TA 360 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8883 (tp30) REVERT: TA 389 MET cc_start: 0.9163 (mtt) cc_final: 0.8801 (mtm) REVERT: TA 394 GLN cc_start: 0.9479 (mt0) cc_final: 0.9151 (mp-120) REVERT: TB 22 SER cc_start: 0.9322 (t) cc_final: 0.8846 (p) REVERT: TB 120 ASP cc_start: 0.8945 (t0) cc_final: 0.8714 (t0) REVERT: TB 131 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7858 (mptt) REVERT: TB 133 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6764 (mtm180) REVERT: TB 138 ASN cc_start: 0.8969 (t0) cc_final: 0.8760 (t0) REVERT: TB 171 ASP cc_start: 0.9405 (t0) cc_final: 0.8684 (p0) REVERT: TB 238 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8725 (ttpp) REVERT: TB 251 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8754 (mt-10) REVERT: TB 272 ASP cc_start: 0.8584 (p0) cc_final: 0.7882 (p0) REVERT: TB 362 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8337 (mm-30) REVERT: LA 120 VAL cc_start: 0.9232 (t) cc_final: 0.9002 (m) REVERT: LA 192 MET cc_start: 0.9385 (tpt) cc_final: 0.7921 (tpp) REVERT: LA 337 ASP cc_start: 0.9154 (m-30) cc_final: 0.8784 (m-30) REVERT: LA 361 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8304 (tp30) REVERT: LA 363 LYS cc_start: 0.8932 (mttt) cc_final: 0.8374 (mtpp) REVERT: LA 378 ARG cc_start: 0.9179 (ptp90) cc_final: 0.8856 (ptp-110) REVERT: LA 379 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (tp) REVERT: LB 126 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8299 (pm20) REVERT: LB 192 MET cc_start: 0.9424 (tpt) cc_final: 0.7419 (mtt) REVERT: LB 293 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: LF 153 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8503 (mt-10) REVERT: LF 192 MET cc_start: 0.6900 (ttp) cc_final: 0.5834 (mmt) REVERT: LF 202 GLU cc_start: 0.9051 (tt0) cc_final: 0.8439 (tm-30) REVERT: LF 206 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8801 (mm-40) REVERT: LF 337 ASP cc_start: 0.9207 (m-30) cc_final: 0.8707 (m-30) REVERT: LF 361 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: LE 133 GLU cc_start: 0.8307 (mp0) cc_final: 0.8088 (mp0) REVERT: LE 192 MET cc_start: 0.8836 (tpt) cc_final: 0.7184 (mtt) REVERT: LE 317 ASP cc_start: 0.8768 (p0) cc_final: 0.8558 (p0) REVERT: LE 361 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: LD 101 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8040 (p90) REVERT: LD 105 ASP cc_start: 0.8372 (m-30) cc_final: 0.7683 (t0) REVERT: LD 120 VAL cc_start: 0.9256 (t) cc_final: 0.8972 (p) REVERT: LD 192 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6750 (mtt) REVERT: LD 197 MET cc_start: 0.4065 (mpt) cc_final: 0.3756 (mpt) REVERT: LD 361 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8816 (tt0) REVERT: LC 171 THR cc_start: 0.9139 (m) cc_final: 0.8803 (p) REVERT: LC 192 MET cc_start: 0.9247 (tpt) cc_final: 0.7465 (mtt) REVERT: LC 197 MET cc_start: 0.9019 (mmm) cc_final: 0.8135 (mpt) REVERT: LC 290 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8385 (mtm-85) outliers start: 97 outliers final: 36 residues processed: 579 average time/residue: 0.5687 time to fit residues: 385.6772 Evaluate side-chains 541 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 494 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 54 THR Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 339 THR Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 297 ILE Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 361 GLU Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LB residue 105 ASP Chi-restraints excluded: chain LB residue 110 ASP Chi-restraints excluded: chain LB residue 122 MET Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 186 SER Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 361 GLU Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 101 PHE Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 301 ILE Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 101 PHE Chi-restraints excluded: chain LC residue 270 GLN Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 33 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 119 optimal weight: 40.0000 chunk 325 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 159 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN TE 83 GLN TF 31 GLN TF 80 GLN TG 31 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 80 GLN TI 83 GLN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 356 ASN LE 376 ASN LD 161 GLN LC 239 GLN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065180 restraints weight = 51232.871| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.39 r_work: 0.2629 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28662 Z= 0.221 Angle : 0.568 8.708 38989 Z= 0.306 Chirality : 0.047 0.278 4385 Planarity : 0.003 0.043 5287 Dihedral : 5.989 62.970 4031 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 16.66 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.13), residues: 3635 helix: 1.51 (0.19), residues: 738 sheet: 0.19 (0.15), residues: 1046 loop : -0.65 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.018 0.001 PHETA 354 TRP 0.017 0.002 TRPTB 65 HIS 0.006 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00491 (28656) covalent geometry : angle 0.56783 (38989) hydrogen bonds : bond 0.04052 ( 820) hydrogen bonds : angle 5.38712 ( 2304) metal coordination : bond 0.00179 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 535 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8629 (t0) cc_final: 0.8389 (t70) REVERT: TC 22 SER cc_start: 0.9098 (t) cc_final: 0.8603 (m) REVERT: TC 120 ASP cc_start: 0.8865 (t0) cc_final: 0.8582 (t0) REVERT: TC 131 LYS cc_start: 0.8350 (mppt) cc_final: 0.8076 (mtmt) REVERT: TC 142 ARG cc_start: 0.8776 (ttm170) cc_final: 0.8467 (tpp80) REVERT: TC 194 ASP cc_start: 0.7686 (t0) cc_final: 0.6874 (t0) REVERT: TC 251 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9181 (mt-10) REVERT: TC 294 ASP cc_start: 0.8926 (m-30) cc_final: 0.8675 (m-30) REVERT: TC 352 CYS cc_start: 0.8743 (t) cc_final: 0.8281 (t) REVERT: TC 372 ASN cc_start: 0.9120 (m-40) cc_final: 0.8144 (p0) REVERT: TC 407 MET cc_start: 0.9361 (mpp) cc_final: 0.8971 (mpp) REVERT: TC 411 ASN cc_start: 0.9288 (m-40) cc_final: 0.8671 (m-40) REVERT: TD 39 GLU cc_start: 0.8938 (tt0) cc_final: 0.8609 (tt0) REVERT: TD 58 ASP cc_start: 0.8986 (t70) cc_final: 0.8522 (t0) REVERT: TD 83 GLN cc_start: 0.9105 (mt0) cc_final: 0.8640 (tt0) REVERT: TD 85 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8626 (mt-10) REVERT: TD 88 ASP cc_start: 0.9106 (t0) cc_final: 0.8882 (t0) REVERT: TE 52 GLU cc_start: 0.9035 (tt0) cc_final: 0.8719 (mt-10) REVERT: TE 58 ASP cc_start: 0.8932 (t70) cc_final: 0.8452 (t70) REVERT: TE 85 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9059 (mt-10) REVERT: TF 7 ASN cc_start: 0.9064 (m-40) cc_final: 0.8847 (m110) REVERT: TF 39 GLU cc_start: 0.8985 (tt0) cc_final: 0.8445 (tt0) REVERT: TF 83 GLN cc_start: 0.8858 (mt0) cc_final: 0.8419 (tt0) REVERT: TF 92 THR cc_start: 0.9706 (m) cc_final: 0.9088 (p) REVERT: TG 7 ASN cc_start: 0.8924 (m-40) cc_final: 0.8576 (m-40) REVERT: TG 71 ASP cc_start: 0.9147 (t0) cc_final: 0.8685 (t0) REVERT: TG 83 GLN cc_start: 0.9137 (mt0) cc_final: 0.8760 (tt0) REVERT: TG 93 TYR cc_start: 0.9219 (m-80) cc_final: 0.8901 (m-80) REVERT: TH 58 ASP cc_start: 0.8962 (t70) cc_final: 0.8651 (t70) REVERT: TH 83 GLN cc_start: 0.9017 (mt0) cc_final: 0.8621 (mt0) REVERT: TH 85 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8789 (mt-10) REVERT: TH 92 THR cc_start: 0.9642 (m) cc_final: 0.9367 (p) REVERT: TA 22 SER cc_start: 0.8933 (t) cc_final: 0.8511 (m) REVERT: TA 112 PHE cc_start: 0.8903 (m-80) cc_final: 0.8689 (m-80) REVERT: TA 143 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8926 (p) REVERT: TA 194 ASP cc_start: 0.8371 (t70) cc_final: 0.7368 (t0) REVERT: TA 222 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: TA 251 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8766 (mt-10) REVERT: TA 280 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8682 (mt-10) REVERT: TA 360 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8903 (tp30) REVERT: TA 367 ASP cc_start: 0.9178 (m-30) cc_final: 0.8892 (m-30) REVERT: TA 372 ASN cc_start: 0.9160 (m-40) cc_final: 0.8413 (m-40) REVERT: TA 389 MET cc_start: 0.9163 (mtt) cc_final: 0.8809 (mtm) REVERT: TB 22 SER cc_start: 0.9337 (t) cc_final: 0.8860 (p) REVERT: TB 65 TRP cc_start: 0.8329 (m-90) cc_final: 0.8052 (m-90) REVERT: TB 120 ASP cc_start: 0.8967 (t0) cc_final: 0.8702 (t0) REVERT: TB 131 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7797 (mptt) REVERT: TB 133 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6976 (mtm110) REVERT: TB 138 ASN cc_start: 0.9009 (t0) cc_final: 0.8779 (t0) REVERT: TB 171 ASP cc_start: 0.9418 (t0) cc_final: 0.8683 (p0) REVERT: TB 178 MET cc_start: 0.9167 (ptm) cc_final: 0.8791 (ppp) REVERT: TB 251 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8815 (mt-10) REVERT: TB 272 ASP cc_start: 0.8610 (p0) cc_final: 0.7943 (p0) REVERT: TB 362 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8420 (mm-30) REVERT: LA 120 VAL cc_start: 0.9221 (t) cc_final: 0.8991 (m) REVERT: LA 192 MET cc_start: 0.9379 (tpt) cc_final: 0.7948 (tpp) REVERT: LA 253 LYS cc_start: 0.9126 (tttp) cc_final: 0.8885 (ttpp) REVERT: LA 281 ASN cc_start: 0.8327 (t0) cc_final: 0.8095 (t0) REVERT: LA 337 ASP cc_start: 0.9105 (m-30) cc_final: 0.8856 (m-30) REVERT: LA 361 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: LA 363 LYS cc_start: 0.8936 (mttt) cc_final: 0.8450 (mtpp) REVERT: LB 107 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9051 (mt-10) REVERT: LB 126 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8335 (pm20) REVERT: LB 192 MET cc_start: 0.9442 (tpt) cc_final: 0.7443 (mtt) REVERT: LB 293 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: LF 117 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8935 (mm) REVERT: LF 153 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8535 (mt-10) REVERT: LF 192 MET cc_start: 0.7010 (ttp) cc_final: 0.5975 (mpt) REVERT: LF 202 GLU cc_start: 0.9052 (tt0) cc_final: 0.8456 (tm-30) REVERT: LF 206 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8806 (mm-40) REVERT: LF 337 ASP cc_start: 0.9179 (m-30) cc_final: 0.8566 (m-30) REVERT: LF 361 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: LF 365 TYR cc_start: 0.9245 (p90) cc_final: 0.8721 (p90) REVERT: LE 133 GLU cc_start: 0.8398 (mp0) cc_final: 0.8173 (mp0) REVERT: LE 192 MET cc_start: 0.8831 (tpt) cc_final: 0.7139 (mtt) REVERT: LE 317 ASP cc_start: 0.8774 (p0) cc_final: 0.8558 (p0) REVERT: LE 337 ASP cc_start: 0.9181 (m-30) cc_final: 0.8907 (m-30) REVERT: LE 361 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8800 (tt0) REVERT: LD 101 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8104 (p90) REVERT: LD 105 ASP cc_start: 0.8371 (m-30) cc_final: 0.7680 (t0) REVERT: LD 120 VAL cc_start: 0.9301 (t) cc_final: 0.9047 (p) REVERT: LD 129 LYS cc_start: 0.9505 (OUTLIER) cc_final: 0.8282 (mttm) REVERT: LD 192 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.6829 (mtt) REVERT: LD 197 MET cc_start: 0.4433 (mpt) cc_final: 0.4138 (mpt) REVERT: LD 361 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8866 (tt0) REVERT: LC 171 THR cc_start: 0.9151 (m) cc_final: 0.8804 (p) REVERT: LC 192 MET cc_start: 0.9276 (tpt) cc_final: 0.7477 (mtt) REVERT: LC 197 MET cc_start: 0.9027 (mmm) cc_final: 0.8178 (mpt) REVERT: LC 290 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8428 (mtm-85) outliers start: 101 outliers final: 40 residues processed: 597 average time/residue: 0.5506 time to fit residues: 386.6483 Evaluate side-chains 565 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 512 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 143 THR Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 168 THR Chi-restraints excluded: chain TB residue 177 THR Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain TB residue 249 THR Chi-restraints excluded: chain TB residue 339 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 297 ILE Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 361 GLU Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LB residue 105 ASP Chi-restraints excluded: chain LB residue 121 VAL Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 117 LEU Chi-restraints excluded: chain LF residue 186 SER Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 361 GLU Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 101 PHE Chi-restraints excluded: chain LD residue 129 LYS Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 22 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 268 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TE 9 GLN TE 83 GLN TF 31 GLN TG 31 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 83 GLN ** TB 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 380 HIS LE 356 ASN LE 376 ASN LE 380 HIS LD 239 GLN LC 239 GLN LC 270 GLN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 380 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.064047 restraints weight = 51405.508| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.39 r_work: 0.2600 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 28662 Z= 0.328 Angle : 0.616 8.232 38989 Z= 0.332 Chirality : 0.048 0.299 4385 Planarity : 0.004 0.043 5287 Dihedral : 5.989 61.102 4031 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.29 % Allowed : 17.68 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.13), residues: 3635 helix: 1.50 (0.19), residues: 734 sheet: 0.02 (0.15), residues: 1062 loop : -0.68 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.018 0.002 PHELE 101 TRP 0.017 0.002 TRPLB 177 HIS 0.008 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00730 (28656) covalent geometry : angle 0.61622 (38989) hydrogen bonds : bond 0.04300 ( 820) hydrogen bonds : angle 5.47862 ( 2304) metal coordination : bond 0.00302 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 506 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8603 (t0) cc_final: 0.8402 (t70) REVERT: TC 22 SER cc_start: 0.9147 (t) cc_final: 0.8668 (m) REVERT: TC 120 ASP cc_start: 0.8970 (t0) cc_final: 0.8741 (t0) REVERT: TC 131 LYS cc_start: 0.8401 (mppt) cc_final: 0.8153 (mtmt) REVERT: TC 142 ARG cc_start: 0.8778 (ttm170) cc_final: 0.8467 (tpp80) REVERT: TC 174 ASN cc_start: 0.8823 (t0) cc_final: 0.8592 (p0) REVERT: TC 179 THR cc_start: 0.8705 (p) cc_final: 0.7988 (t) REVERT: TC 194 ASP cc_start: 0.7593 (t0) cc_final: 0.6808 (t0) REVERT: TC 251 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9128 (mt-10) REVERT: TC 319 MET cc_start: 0.9271 (tmm) cc_final: 0.8942 (tmm) REVERT: TC 352 CYS cc_start: 0.8791 (t) cc_final: 0.8399 (t) REVERT: TC 367 ASP cc_start: 0.9157 (m-30) cc_final: 0.8585 (m-30) REVERT: TC 372 ASN cc_start: 0.9098 (m-40) cc_final: 0.8141 (p0) REVERT: TC 407 MET cc_start: 0.9372 (mpp) cc_final: 0.8984 (mpp) REVERT: TC 411 ASN cc_start: 0.9286 (m-40) cc_final: 0.8660 (m-40) REVERT: TD 39 GLU cc_start: 0.8999 (tt0) cc_final: 0.8679 (tt0) REVERT: TD 58 ASP cc_start: 0.9006 (t70) cc_final: 0.8504 (t0) REVERT: TD 65 ASP cc_start: 0.8945 (t0) cc_final: 0.8657 (t0) REVERT: TD 83 GLN cc_start: 0.9175 (mt0) cc_final: 0.8664 (tt0) REVERT: TD 85 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8601 (mt-10) REVERT: TD 88 ASP cc_start: 0.9144 (t0) cc_final: 0.8938 (t0) REVERT: TE 58 ASP cc_start: 0.8925 (t70) cc_final: 0.8438 (t70) REVERT: TE 85 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8981 (mt-10) REVERT: TF 7 ASN cc_start: 0.9154 (m-40) cc_final: 0.8945 (m110) REVERT: TF 83 GLN cc_start: 0.8962 (mt0) cc_final: 0.8352 (tt0) REVERT: TG 7 ASN cc_start: 0.8946 (m-40) cc_final: 0.8612 (m-40) REVERT: TG 71 ASP cc_start: 0.9143 (t0) cc_final: 0.8637 (t0) REVERT: TG 83 GLN cc_start: 0.9250 (mt0) cc_final: 0.8871 (tt0) REVERT: TG 93 TYR cc_start: 0.9221 (m-80) cc_final: 0.8917 (m-80) REVERT: TH 58 ASP cc_start: 0.8959 (t70) cc_final: 0.8633 (t70) REVERT: TH 83 GLN cc_start: 0.9046 (mt0) cc_final: 0.8660 (mt0) REVERT: TH 85 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8951 (mt-10) REVERT: TH 92 THR cc_start: 0.9634 (m) cc_final: 0.9373 (p) REVERT: TA 22 SER cc_start: 0.8958 (t) cc_final: 0.8545 (m) REVERT: TA 48 LEU cc_start: 0.9616 (mp) cc_final: 0.9402 (mm) REVERT: TA 112 PHE cc_start: 0.8992 (m-80) cc_final: 0.8738 (m-80) REVERT: TA 131 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8372 (mppt) REVERT: TA 143 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8922 (p) REVERT: TA 155 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8745 (tp30) REVERT: TA 194 ASP cc_start: 0.8385 (t70) cc_final: 0.7407 (t0) REVERT: TA 222 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: TA 251 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8737 (mt-10) REVERT: TA 280 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8710 (mt-10) REVERT: TA 360 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8906 (tp30) REVERT: TA 367 ASP cc_start: 0.9179 (m-30) cc_final: 0.8917 (m-30) REVERT: TA 372 ASN cc_start: 0.9075 (m-40) cc_final: 0.8269 (m-40) REVERT: TA 389 MET cc_start: 0.9152 (mtt) cc_final: 0.8761 (mtm) REVERT: TB 22 SER cc_start: 0.9343 (t) cc_final: 0.8870 (p) REVERT: TB 131 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7850 (mptt) REVERT: TB 133 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6763 (mtm180) REVERT: TB 171 ASP cc_start: 0.9431 (t0) cc_final: 0.9152 (t0) REVERT: TB 194 ASP cc_start: 0.8477 (m-30) cc_final: 0.8103 (m-30) REVERT: TB 251 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8864 (mt-10) REVERT: TB 272 ASP cc_start: 0.8531 (p0) cc_final: 0.7890 (p0) REVERT: TB 283 ASP cc_start: 0.8638 (p0) cc_final: 0.8365 (p0) REVERT: TB 362 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8388 (mm-30) REVERT: TB 389 MET cc_start: 0.9285 (mtp) cc_final: 0.9019 (ttm) REVERT: LA 192 MET cc_start: 0.9387 (tpt) cc_final: 0.7805 (mtt) REVERT: LA 202 GLU cc_start: 0.9002 (tt0) cc_final: 0.8653 (tp30) REVERT: LA 253 LYS cc_start: 0.9149 (tttp) cc_final: 0.8921 (ttpp) REVERT: LA 281 ASN cc_start: 0.8206 (t0) cc_final: 0.7959 (t0) REVERT: LA 337 ASP cc_start: 0.9069 (m-30) cc_final: 0.8838 (m-30) REVERT: LA 361 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: LA 363 LYS cc_start: 0.8977 (mttt) cc_final: 0.8488 (mtpp) REVERT: LA 379 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8883 (tp) REVERT: LB 126 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8336 (pm20) REVERT: LB 192 MET cc_start: 0.9447 (tpt) cc_final: 0.7417 (mtt) REVERT: LB 293 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (pt0) REVERT: LF 117 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8899 (mm) REVERT: LF 153 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8512 (mt-10) REVERT: LF 192 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.5797 (mpt) REVERT: LF 202 GLU cc_start: 0.9058 (tt0) cc_final: 0.8466 (tm-30) REVERT: LF 206 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8846 (mm-40) REVERT: LF 337 ASP cc_start: 0.9213 (m-30) cc_final: 0.8729 (m-30) REVERT: LF 361 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: LF 365 TYR cc_start: 0.9296 (p90) cc_final: 0.8733 (p90) REVERT: LE 133 GLU cc_start: 0.8476 (mp0) cc_final: 0.8247 (mp0) REVERT: LE 192 MET cc_start: 0.8847 (tpt) cc_final: 0.7164 (mtt) REVERT: LE 317 ASP cc_start: 0.8854 (p0) cc_final: 0.8634 (p0) REVERT: LE 361 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8817 (tt0) REVERT: LD 101 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8183 (p90) REVERT: LD 105 ASP cc_start: 0.8437 (m-30) cc_final: 0.7758 (t0) REVERT: LD 120 VAL cc_start: 0.9309 (t) cc_final: 0.9091 (p) REVERT: LD 129 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.8269 (mttm) REVERT: LD 192 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.6769 (mtt) REVERT: LD 197 MET cc_start: 0.4436 (mpt) cc_final: 0.3860 (mpt) REVERT: LD 361 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8855 (tt0) REVERT: LC 171 THR cc_start: 0.9166 (m) cc_final: 0.8831 (p) REVERT: LC 192 MET cc_start: 0.9290 (tpt) cc_final: 0.7455 (mtt) REVERT: LC 197 MET cc_start: 0.9107 (mmm) cc_final: 0.8300 (mpt) REVERT: LC 358 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: LC 366 GLU cc_start: 0.9058 (mp0) cc_final: 0.8807 (mm-30) outliers start: 100 outliers final: 50 residues processed: 570 average time/residue: 0.5585 time to fit residues: 374.5535 Evaluate side-chains 562 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 496 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TI residue 7 ASN Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 143 THR Chi-restraints excluded: chain TA residue 155 GLU Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 168 THR Chi-restraints excluded: chain TB residue 177 THR Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain TB residue 247 LEU Chi-restraints excluded: chain TB residue 249 THR Chi-restraints excluded: chain TB residue 339 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 297 ILE Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 361 GLU Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LB residue 105 ASP Chi-restraints excluded: chain LB residue 121 VAL Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 117 LEU Chi-restraints excluded: chain LF residue 186 SER Chi-restraints excluded: chain LF residue 192 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 361 GLU Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 101 PHE Chi-restraints excluded: chain LD residue 129 LYS Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 301 ILE Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 270 GLN Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 306 MET Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 358 GLN Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 97 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 278 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 105 GLN TD 31 GLN TE 83 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TG 31 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 83 GLN TB 138 ASN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 270 GLN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 356 ASN LE 376 ASN LC 270 GLN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067617 restraints weight = 50835.261| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.40 r_work: 0.2665 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28662 Z= 0.146 Angle : 0.547 7.890 38989 Z= 0.295 Chirality : 0.045 0.312 4385 Planarity : 0.003 0.045 5287 Dihedral : 5.833 67.027 4031 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.96 % Allowed : 18.47 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.13), residues: 3635 helix: 1.73 (0.19), residues: 721 sheet: 0.20 (0.16), residues: 1022 loop : -0.69 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.017 0.001 PHETA 354 TRP 0.023 0.001 TRPTB 65 HIS 0.005 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00323 (28656) covalent geometry : angle 0.54678 (38989) hydrogen bonds : bond 0.03701 ( 820) hydrogen bonds : angle 5.29176 ( 2304) metal coordination : bond 0.00079 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 572 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8695 (t0) cc_final: 0.8379 (t70) REVERT: TC 22 SER cc_start: 0.9103 (t) cc_final: 0.8593 (m) REVERT: TC 120 ASP cc_start: 0.8995 (t0) cc_final: 0.8711 (t0) REVERT: TC 131 LYS cc_start: 0.8370 (mppt) cc_final: 0.8074 (mtmt) REVERT: TC 142 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8422 (tpp80) REVERT: TC 179 THR cc_start: 0.8659 (p) cc_final: 0.7899 (t) REVERT: TC 194 ASP cc_start: 0.7776 (t0) cc_final: 0.6959 (t0) REVERT: TC 251 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9207 (mt-10) REVERT: TC 352 CYS cc_start: 0.8716 (t) cc_final: 0.8226 (t) REVERT: TC 363 GLN cc_start: 0.9165 (tp40) cc_final: 0.8405 (tp40) REVERT: TC 367 ASP cc_start: 0.9154 (m-30) cc_final: 0.8155 (m-30) REVERT: TC 372 ASN cc_start: 0.9095 (m-40) cc_final: 0.8218 (p0) REVERT: TC 407 MET cc_start: 0.9347 (mpp) cc_final: 0.9003 (mpp) REVERT: TC 411 ASN cc_start: 0.9242 (m-40) cc_final: 0.8646 (m-40) REVERT: TD 39 GLU cc_start: 0.8911 (tt0) cc_final: 0.8613 (tt0) REVERT: TD 58 ASP cc_start: 0.9004 (t70) cc_final: 0.8516 (t70) REVERT: TD 83 GLN cc_start: 0.9080 (mt0) cc_final: 0.8641 (tt0) REVERT: TD 85 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8617 (mt-10) REVERT: TD 88 ASP cc_start: 0.9048 (t0) cc_final: 0.8809 (t0) REVERT: TE 58 ASP cc_start: 0.8905 (t70) cc_final: 0.8438 (t70) REVERT: TE 85 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9011 (mt-10) REVERT: TF 83 GLN cc_start: 0.8674 (mt0) cc_final: 0.8059 (tt0) REVERT: TG 58 ASP cc_start: 0.9033 (t70) cc_final: 0.8700 (t0) REVERT: TG 71 ASP cc_start: 0.9124 (t0) cc_final: 0.8683 (t0) REVERT: TG 83 GLN cc_start: 0.9083 (mt0) cc_final: 0.8725 (tt0) REVERT: TG 105 ASP cc_start: 0.9069 (m-30) cc_final: 0.8643 (m-30) REVERT: TH 58 ASP cc_start: 0.8983 (t70) cc_final: 0.8655 (t70) REVERT: TH 83 GLN cc_start: 0.8949 (mt0) cc_final: 0.8563 (mt0) REVERT: TH 85 GLU cc_start: 0.9360 (mt-10) cc_final: 0.8768 (mt-10) REVERT: TH 92 THR cc_start: 0.9638 (m) cc_final: 0.9270 (p) REVERT: TI 111 ARG cc_start: 0.9141 (mtm-85) cc_final: 0.8920 (tpp80) REVERT: TA 48 LEU cc_start: 0.9513 (mp) cc_final: 0.9307 (mm) REVERT: TA 112 PHE cc_start: 0.8962 (m-80) cc_final: 0.8751 (m-80) REVERT: TA 131 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8141 (mppt) REVERT: TA 143 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8903 (p) REVERT: TA 155 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8697 (tp30) REVERT: TA 194 ASP cc_start: 0.8307 (t70) cc_final: 0.7319 (t0) REVERT: TA 222 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: TA 251 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8775 (mt-10) REVERT: TA 280 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8670 (mt-10) REVERT: TA 360 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8890 (tp30) REVERT: TA 367 ASP cc_start: 0.9145 (m-30) cc_final: 0.8858 (m-30) REVERT: TA 372 ASN cc_start: 0.9016 (m-40) cc_final: 0.8142 (m-40) REVERT: TA 389 MET cc_start: 0.9128 (mtt) cc_final: 0.8758 (mtm) REVERT: TB 22 SER cc_start: 0.9303 (t) cc_final: 0.8828 (p) REVERT: TB 98 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.8233 (ptp-110) REVERT: TB 131 LYS cc_start: 0.8147 (mtmt) cc_final: 0.7818 (mptt) REVERT: TB 133 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6770 (mtm180) REVERT: TB 171 ASP cc_start: 0.9437 (t0) cc_final: 0.8700 (p0) REVERT: TB 217 ASP cc_start: 0.9155 (m-30) cc_final: 0.8918 (m-30) REVERT: TB 251 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8999 (mt-10) REVERT: TB 254 ASP cc_start: 0.9408 (m-30) cc_final: 0.9186 (m-30) REVERT: TB 272 ASP cc_start: 0.8531 (p0) cc_final: 0.7888 (p0) REVERT: TB 362 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8375 (mm-30) REVERT: TB 367 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.9091 (t0) REVERT: LA 192 MET cc_start: 0.9346 (tpt) cc_final: 0.7899 (tpp) REVERT: LA 281 ASN cc_start: 0.8090 (t0) cc_final: 0.7807 (t0) REVERT: LA 337 ASP cc_start: 0.8995 (m-30) cc_final: 0.8682 (m-30) REVERT: LA 361 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8181 (tp30) REVERT: LA 363 LYS cc_start: 0.8995 (mttt) cc_final: 0.8482 (mtpp) REVERT: LB 119 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8811 (pm20) REVERT: LB 126 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8269 (pm20) REVERT: LB 192 MET cc_start: 0.9431 (tpt) cc_final: 0.7391 (mtt) REVERT: LB 202 GLU cc_start: 0.9006 (tp30) cc_final: 0.8716 (tp30) REVERT: LF 153 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8471 (mt-10) REVERT: LF 192 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5849 (mpt) REVERT: LF 202 GLU cc_start: 0.9044 (tt0) cc_final: 0.8416 (tm-30) REVERT: LF 206 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8775 (mm-40) REVERT: LF 337 ASP cc_start: 0.9119 (m-30) cc_final: 0.8507 (m-30) REVERT: LF 361 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: LF 365 TYR cc_start: 0.9332 (p90) cc_final: 0.8809 (p90) REVERT: LE 122 MET cc_start: 0.9546 (mmt) cc_final: 0.9149 (mmm) REVERT: LE 133 GLU cc_start: 0.8422 (mp0) cc_final: 0.8188 (mp0) REVERT: LE 192 MET cc_start: 0.8836 (tpt) cc_final: 0.7078 (mtt) REVERT: LE 317 ASP cc_start: 0.8787 (p0) cc_final: 0.8565 (p0) REVERT: LE 337 ASP cc_start: 0.9151 (m-30) cc_final: 0.8900 (m-30) REVERT: LE 361 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8833 (tt0) REVERT: LD 105 ASP cc_start: 0.8338 (m-30) cc_final: 0.7646 (t0) REVERT: LD 192 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.6843 (mtt) REVERT: LD 361 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: LD 367 ASP cc_start: 0.8995 (t0) cc_final: 0.8711 (t0) REVERT: LC 122 MET cc_start: 0.9469 (mmp) cc_final: 0.9239 (mmm) REVERT: LC 171 THR cc_start: 0.9124 (m) cc_final: 0.8771 (p) REVERT: LC 192 MET cc_start: 0.9277 (tpt) cc_final: 0.7455 (mtt) REVERT: LC 197 MET cc_start: 0.9039 (mmm) cc_final: 0.8115 (mpt) REVERT: LC 290 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8460 (mtm-85) REVERT: LC 358 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: LC 366 GLU cc_start: 0.9015 (mp0) cc_final: 0.8796 (mm-30) outliers start: 90 outliers final: 45 residues processed: 630 average time/residue: 0.5717 time to fit residues: 425.0123 Evaluate side-chains 585 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 528 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 128 THR Chi-restraints excluded: chain TC residue 172 VAL Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 9 GLN Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 34 LYS Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TA residue 21 GLU Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 143 THR Chi-restraints excluded: chain TA residue 155 GLU Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 128 THR Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 168 THR Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 379 LEU Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LF residue 192 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 105 ASP Chi-restraints excluded: chain LE residue 171 THR Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 356 ASN Chi-restraints excluded: chain LE residue 361 GLU Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 270 GLN Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 358 GLN Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 187 optimal weight: 8.9990 chunk 245 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 270 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 83 GLN TF 31 GLN TF 80 GLN TG 31 GLN TG 80 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 31 GLN TI 83 GLN TB 138 ASN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 356 ASN LE 376 ASN LC 239 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067350 restraints weight = 51242.540| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.41 r_work: 0.2666 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28662 Z= 0.167 Angle : 0.558 7.684 38989 Z= 0.300 Chirality : 0.046 0.356 4385 Planarity : 0.003 0.045 5287 Dihedral : 5.746 65.951 4028 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.63 % Allowed : 19.55 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 3635 helix: 1.70 (0.19), residues: 728 sheet: 0.20 (0.16), residues: 1016 loop : -0.67 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.023 0.001 PHETA 163 TRP 0.028 0.002 TRPTB 65 HIS 0.005 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00374 (28656) covalent geometry : angle 0.55765 (38989) hydrogen bonds : bond 0.03761 ( 820) hydrogen bonds : angle 5.31139 ( 2304) metal coordination : bond 0.00109 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 547 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8592 (t0) cc_final: 0.8197 (t70) REVERT: TC 22 SER cc_start: 0.9113 (t) cc_final: 0.8593 (m) REVERT: TC 114 MET cc_start: 0.8711 (ttp) cc_final: 0.8277 (tmm) REVERT: TC 117 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7152 (ttpp) REVERT: TC 120 ASP cc_start: 0.9004 (t0) cc_final: 0.8704 (t0) REVERT: TC 131 LYS cc_start: 0.8367 (mppt) cc_final: 0.8086 (mtmt) REVERT: TC 142 ARG cc_start: 0.8789 (ttm170) cc_final: 0.8407 (tpp80) REVERT: TC 179 THR cc_start: 0.8555 (p) cc_final: 0.7778 (t) REVERT: TC 251 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9182 (mt-10) REVERT: TC 352 CYS cc_start: 0.8735 (t) cc_final: 0.8264 (t) REVERT: TC 363 GLN cc_start: 0.9173 (tp40) cc_final: 0.8389 (tp40) REVERT: TC 367 ASP cc_start: 0.9153 (m-30) cc_final: 0.8161 (m-30) REVERT: TC 372 ASN cc_start: 0.9076 (m-40) cc_final: 0.8259 (p0) REVERT: TC 407 MET cc_start: 0.9354 (mpp) cc_final: 0.9004 (mpp) REVERT: TC 411 ASN cc_start: 0.9235 (m-40) cc_final: 0.8638 (m-40) REVERT: TD 39 GLU cc_start: 0.8927 (tt0) cc_final: 0.8569 (tt0) REVERT: TD 58 ASP cc_start: 0.9006 (t70) cc_final: 0.8494 (t0) REVERT: TD 83 GLN cc_start: 0.9078 (mt0) cc_final: 0.8563 (tt0) REVERT: TD 85 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8541 (mt-10) REVERT: TD 88 ASP cc_start: 0.9046 (t0) cc_final: 0.8810 (t0) REVERT: TE 58 ASP cc_start: 0.8910 (t70) cc_final: 0.8434 (t70) REVERT: TF 39 GLU cc_start: 0.9021 (tt0) cc_final: 0.8615 (tt0) REVERT: TF 83 GLN cc_start: 0.8772 (mt0) cc_final: 0.8318 (tt0) REVERT: TG 24 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9042 (mm-30) REVERT: TG 58 ASP cc_start: 0.9006 (t70) cc_final: 0.8668 (t0) REVERT: TG 71 ASP cc_start: 0.9130 (t0) cc_final: 0.8837 (t0) REVERT: TG 83 GLN cc_start: 0.9083 (mt0) cc_final: 0.8790 (tt0) REVERT: TH 58 ASP cc_start: 0.8996 (t70) cc_final: 0.8653 (t70) REVERT: TH 83 GLN cc_start: 0.8964 (mt0) cc_final: 0.8569 (mt0) REVERT: TH 85 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8925 (mt-10) REVERT: TH 92 THR cc_start: 0.9645 (m) cc_final: 0.9377 (p) REVERT: TA 48 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9292 (mm) REVERT: TA 97 ILE cc_start: 0.9565 (pt) cc_final: 0.9286 (pp) REVERT: TA 112 PHE cc_start: 0.8972 (m-80) cc_final: 0.8766 (m-80) REVERT: TA 116 LEU cc_start: 0.8895 (tp) cc_final: 0.8544 (pp) REVERT: TA 131 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8439 (mppt) REVERT: TA 155 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: TA 194 ASP cc_start: 0.8314 (t70) cc_final: 0.7375 (t0) REVERT: TA 222 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: TA 251 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8890 (mt-10) REVERT: TA 280 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8665 (mt-10) REVERT: TA 360 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8912 (tp30) REVERT: TA 367 ASP cc_start: 0.9081 (m-30) cc_final: 0.8850 (m-30) REVERT: TA 389 MET cc_start: 0.9129 (mtt) cc_final: 0.8751 (mtm) REVERT: TB 22 SER cc_start: 0.9317 (t) cc_final: 0.8846 (p) REVERT: TB 131 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7930 (mptt) REVERT: TB 133 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6894 (mtm180) REVERT: TB 138 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8305 (p0) REVERT: TB 171 ASP cc_start: 0.9432 (t0) cc_final: 0.8674 (p0) REVERT: TB 178 MET cc_start: 0.9162 (ptm) cc_final: 0.8827 (pmm) REVERT: TB 254 ASP cc_start: 0.9417 (m-30) cc_final: 0.9154 (m-30) REVERT: TB 272 ASP cc_start: 0.8530 (p0) cc_final: 0.7915 (p0) REVERT: TB 362 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8463 (mm-30) REVERT: TB 367 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.9036 (t0) REVERT: LA 192 MET cc_start: 0.9343 (tpt) cc_final: 0.7897 (tpp) REVERT: LA 281 ASN cc_start: 0.8072 (t0) cc_final: 0.7758 (t0) REVERT: LA 310 MET cc_start: 0.9624 (mtp) cc_final: 0.9412 (mmt) REVERT: LA 337 ASP cc_start: 0.9032 (m-30) cc_final: 0.8697 (m-30) REVERT: LA 361 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8148 (tp30) REVERT: LA 363 LYS cc_start: 0.8908 (mttt) cc_final: 0.8417 (mtpp) REVERT: LB 119 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8819 (pm20) REVERT: LB 126 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8272 (pm20) REVERT: LB 192 MET cc_start: 0.9431 (tpt) cc_final: 0.7387 (mtt) REVERT: LB 202 GLU cc_start: 0.9022 (tp30) cc_final: 0.8748 (tp30) REVERT: LF 153 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8527 (mt-10) REVERT: LF 192 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.5726 (mpt) REVERT: LF 195 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8961 (mm-40) REVERT: LF 202 GLU cc_start: 0.9044 (tt0) cc_final: 0.8368 (tp30) REVERT: LF 206 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8629 (mm110) REVERT: LF 337 ASP cc_start: 0.9167 (m-30) cc_final: 0.8539 (m-30) REVERT: LF 361 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: LF 365 TYR cc_start: 0.9344 (p90) cc_final: 0.8855 (p90) REVERT: LE 122 MET cc_start: 0.9541 (mmt) cc_final: 0.9150 (mmm) REVERT: LE 133 GLU cc_start: 0.8432 (mp0) cc_final: 0.8205 (mp0) REVERT: LE 192 MET cc_start: 0.8837 (tpt) cc_final: 0.7072 (mtt) REVERT: LE 197 MET cc_start: 0.8615 (mmt) cc_final: 0.7724 (mpt) REVERT: LE 317 ASP cc_start: 0.8804 (p0) cc_final: 0.8578 (p0) REVERT: LE 337 ASP cc_start: 0.9136 (m-30) cc_final: 0.8855 (m-30) REVERT: LD 105 ASP cc_start: 0.8356 (m-30) cc_final: 0.7659 (t0) REVERT: LD 192 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6837 (mtt) REVERT: LD 197 MET cc_start: 0.4158 (mpt) cc_final: 0.3906 (mpt) REVERT: LD 253 LYS cc_start: 0.9310 (ttmt) cc_final: 0.9096 (ttmt) REVERT: LD 361 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8769 (tt0) REVERT: LC 171 THR cc_start: 0.9134 (m) cc_final: 0.8775 (p) REVERT: LC 192 MET cc_start: 0.9275 (tpt) cc_final: 0.7456 (mtt) REVERT: LC 197 MET cc_start: 0.8964 (mmm) cc_final: 0.8300 (mpt) REVERT: LC 290 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8481 (mtm-85) REVERT: LC 366 GLU cc_start: 0.9027 (mp0) cc_final: 0.8810 (mm-30) outliers start: 80 outliers final: 39 residues processed: 600 average time/residue: 0.5796 time to fit residues: 410.1716 Evaluate side-chains 577 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 527 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 128 THR Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 28 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 48 LEU Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 128 THR Chi-restraints excluded: chain TA residue 155 GLU Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 138 ASN Chi-restraints excluded: chain TB residue 168 THR Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain TB residue 249 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 297 ILE Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LF residue 192 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 375 VAL Chi-restraints excluded: chain LC residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 47 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 183 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 274 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 105 GLN TD 31 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 31 GLN TG 80 GLN TI 9 GLN TI 31 GLN TI 83 GLN TA 260 HIS TB 138 ASN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 376 ASN ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.065901 restraints weight = 51248.712| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.37 r_work: 0.2648 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28662 Z= 0.223 Angle : 0.594 12.191 38989 Z= 0.317 Chirality : 0.047 0.266 4385 Planarity : 0.004 0.045 5287 Dihedral : 5.746 64.167 4028 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.40 % Allowed : 20.14 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.14), residues: 3635 helix: 1.55 (0.19), residues: 745 sheet: 0.15 (0.16), residues: 1022 loop : -0.64 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.015 0.001 PHETA 163 TRP 0.032 0.002 TRPTB 65 HIS 0.006 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00499 (28656) covalent geometry : angle 0.59389 (38989) hydrogen bonds : bond 0.03938 ( 820) hydrogen bonds : angle 5.37375 ( 2304) metal coordination : bond 0.00152 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 527 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8642 (t0) cc_final: 0.8365 (t70) REVERT: TC 22 SER cc_start: 0.9099 (t) cc_final: 0.8580 (m) REVERT: TC 114 MET cc_start: 0.8550 (ttp) cc_final: 0.8321 (tpp) REVERT: TC 120 ASP cc_start: 0.9021 (t0) cc_final: 0.8732 (t0) REVERT: TC 131 LYS cc_start: 0.8343 (mppt) cc_final: 0.8078 (mtmt) REVERT: TC 142 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8409 (tpp80) REVERT: TC 179 THR cc_start: 0.8544 (p) cc_final: 0.7781 (t) REVERT: TC 218 LYS cc_start: 0.8553 (mttp) cc_final: 0.8278 (mtmm) REVERT: TC 238 LYS cc_start: 0.8972 (ptmt) cc_final: 0.8686 (ptmm) REVERT: TC 251 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9155 (mt-10) REVERT: TC 352 CYS cc_start: 0.8750 (t) cc_final: 0.8277 (t) REVERT: TC 363 GLN cc_start: 0.9169 (tp40) cc_final: 0.8390 (tp40) REVERT: TC 367 ASP cc_start: 0.9170 (m-30) cc_final: 0.8213 (m-30) REVERT: TC 372 ASN cc_start: 0.9077 (m-40) cc_final: 0.8271 (p0) REVERT: TC 407 MET cc_start: 0.9350 (mpp) cc_final: 0.9006 (mpp) REVERT: TC 411 ASN cc_start: 0.9246 (m-40) cc_final: 0.8648 (m-40) REVERT: TD 34 LYS cc_start: 0.9320 (ttpp) cc_final: 0.9111 (tttp) REVERT: TD 39 GLU cc_start: 0.8936 (tt0) cc_final: 0.8632 (tt0) REVERT: TD 58 ASP cc_start: 0.9011 (t70) cc_final: 0.8487 (t70) REVERT: TD 61 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8453 (mt-10) REVERT: TD 83 GLN cc_start: 0.9067 (mt0) cc_final: 0.8623 (tt0) REVERT: TD 85 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8602 (mt-10) REVERT: TD 88 ASP cc_start: 0.9071 (t0) cc_final: 0.8858 (t0) REVERT: TE 58 ASP cc_start: 0.8904 (t70) cc_final: 0.8415 (t70) REVERT: TE 85 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8684 (mt-10) REVERT: TF 39 GLU cc_start: 0.9031 (tt0) cc_final: 0.8655 (tt0) REVERT: TF 83 GLN cc_start: 0.8791 (mt0) cc_final: 0.8243 (tt0) REVERT: TG 24 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9050 (mm-30) REVERT: TG 58 ASP cc_start: 0.8992 (t70) cc_final: 0.8642 (t0) REVERT: TG 71 ASP cc_start: 0.9118 (t0) cc_final: 0.8662 (t0) REVERT: TG 83 GLN cc_start: 0.9110 (mt0) cc_final: 0.8757 (tt0) REVERT: TH 58 ASP cc_start: 0.8957 (t70) cc_final: 0.8599 (t70) REVERT: TH 83 GLN cc_start: 0.8961 (mt0) cc_final: 0.8565 (mt0) REVERT: TH 85 GLU cc_start: 0.9405 (mt-10) cc_final: 0.8744 (mt-10) REVERT: TH 92 THR cc_start: 0.9638 (m) cc_final: 0.9364 (p) REVERT: TI 11 SER cc_start: 0.9046 (m) cc_final: 0.8736 (t) REVERT: TA 48 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9298 (mm) REVERT: TA 97 ILE cc_start: 0.9570 (pt) cc_final: 0.9299 (pp) REVERT: TA 112 PHE cc_start: 0.9013 (m-80) cc_final: 0.8803 (m-80) REVERT: TA 131 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8355 (mppt) REVERT: TA 155 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8711 (tp30) REVERT: TA 194 ASP cc_start: 0.8330 (t70) cc_final: 0.7410 (t0) REVERT: TA 222 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: TA 251 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8825 (mt-10) REVERT: TA 280 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8767 (mt-10) REVERT: TA 360 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8924 (tp30) REVERT: TA 367 ASP cc_start: 0.9091 (m-30) cc_final: 0.8867 (m-30) REVERT: TA 389 MET cc_start: 0.9128 (mtt) cc_final: 0.8701 (mtm) REVERT: TB 22 SER cc_start: 0.9318 (t) cc_final: 0.8843 (p) REVERT: TB 65 TRP cc_start: 0.8263 (m-90) cc_final: 0.7909 (m-90) REVERT: TB 131 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7953 (mptt) REVERT: TB 133 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6893 (mtm180) REVERT: TB 138 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8508 (p0) REVERT: TB 171 ASP cc_start: 0.9437 (t0) cc_final: 0.8683 (p0) REVERT: TB 178 MET cc_start: 0.9200 (ptm) cc_final: 0.8808 (pmm) REVERT: TB 246 LYS cc_start: 0.9083 (mptp) cc_final: 0.8628 (mmtt) REVERT: TB 254 ASP cc_start: 0.9432 (m-30) cc_final: 0.9149 (m-30) REVERT: TB 272 ASP cc_start: 0.8523 (p0) cc_final: 0.7905 (p0) REVERT: TB 362 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8473 (mm-30) REVERT: TB 367 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.9035 (t0) REVERT: LA 192 MET cc_start: 0.9339 (tpt) cc_final: 0.7899 (tpp) REVERT: LA 281 ASN cc_start: 0.8103 (t0) cc_final: 0.7801 (t0) REVERT: LA 337 ASP cc_start: 0.9021 (m-30) cc_final: 0.8688 (m-30) REVERT: LA 361 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8176 (tp30) REVERT: LA 363 LYS cc_start: 0.8882 (mttt) cc_final: 0.8380 (mtpp) REVERT: LB 119 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8807 (pm20) REVERT: LB 126 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8252 (pm20) REVERT: LB 164 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7334 (mm-30) REVERT: LB 192 MET cc_start: 0.9419 (tpt) cc_final: 0.7357 (mtt) REVERT: LB 202 GLU cc_start: 0.9049 (tp30) cc_final: 0.8741 (tp30) REVERT: LF 153 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8567 (mt-10) REVERT: LF 192 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5535 (mpt) REVERT: LF 202 GLU cc_start: 0.9038 (tt0) cc_final: 0.8343 (tp30) REVERT: LF 206 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8648 (mm110) REVERT: LF 337 ASP cc_start: 0.9175 (m-30) cc_final: 0.8532 (m-30) REVERT: LF 361 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: LF 365 TYR cc_start: 0.9345 (p90) cc_final: 0.8817 (p90) REVERT: LE 133 GLU cc_start: 0.8406 (mp0) cc_final: 0.8174 (mp0) REVERT: LE 192 MET cc_start: 0.8824 (tpt) cc_final: 0.7072 (mtt) REVERT: LE 317 ASP cc_start: 0.8835 (p0) cc_final: 0.8615 (p0) REVERT: LE 337 ASP cc_start: 0.9150 (m-30) cc_final: 0.8881 (m-30) REVERT: LD 105 ASP cc_start: 0.8396 (m-30) cc_final: 0.7681 (t0) REVERT: LD 192 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6658 (mtt) REVERT: LD 361 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: LD 367 ASP cc_start: 0.8978 (t0) cc_final: 0.8721 (t0) REVERT: LC 171 THR cc_start: 0.9165 (m) cc_final: 0.8798 (p) REVERT: LC 192 MET cc_start: 0.9259 (tpt) cc_final: 0.7420 (mtt) REVERT: LC 197 MET cc_start: 0.8984 (mmm) cc_final: 0.8229 (mpt) REVERT: LC 290 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8440 (mtm-85) REVERT: LC 366 GLU cc_start: 0.9024 (mp0) cc_final: 0.8789 (mm-30) outliers start: 73 outliers final: 41 residues processed: 578 average time/residue: 0.5603 time to fit residues: 380.7353 Evaluate side-chains 559 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 507 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 128 THR Chi-restraints excluded: chain TC residue 172 VAL Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TH residue 84 ILE Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 48 LEU Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 124 SER Chi-restraints excluded: chain TA residue 128 THR Chi-restraints excluded: chain TA residue 155 GLU Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 128 THR Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 138 ASN Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LB residue 201 ILE Chi-restraints excluded: chain LF residue 192 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 105 ASP Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 7.9990 chunk 165 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 chunk 219 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN TG 31 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 31 GLN TI 83 GLN TA 260 HIS TB 138 ASN ** TB 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 356 ASN LE 376 ASN ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063942 restraints weight = 51305.837| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.36 r_work: 0.2606 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 28662 Z= 0.333 Angle : 0.655 13.480 38989 Z= 0.349 Chirality : 0.049 0.233 4385 Planarity : 0.004 0.045 5287 Dihedral : 5.848 61.729 4028 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.10 % Allowed : 20.57 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.13), residues: 3635 helix: 1.41 (0.19), residues: 737 sheet: 0.06 (0.16), residues: 1028 loop : -0.69 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGLB 193 TYR 0.030 0.002 TYRTB 410 PHE 0.019 0.002 PHELE 101 TRP 0.028 0.002 TRPTB 65 HIS 0.008 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00741 (28656) covalent geometry : angle 0.65514 (38989) hydrogen bonds : bond 0.04305 ( 820) hydrogen bonds : angle 5.53729 ( 2304) metal coordination : bond 0.00267 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 501 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8634 (t0) cc_final: 0.8433 (t70) REVERT: TC 22 SER cc_start: 0.9154 (t) cc_final: 0.8672 (m) REVERT: TC 120 ASP cc_start: 0.8960 (t0) cc_final: 0.8652 (t0) REVERT: TC 131 LYS cc_start: 0.8398 (mppt) cc_final: 0.8129 (mtmt) REVERT: TC 142 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8397 (tpp80) REVERT: TC 174 ASN cc_start: 0.8795 (t0) cc_final: 0.8553 (p0) REVERT: TC 218 LYS cc_start: 0.8490 (mttp) cc_final: 0.8220 (mtmm) REVERT: TC 238 LYS cc_start: 0.9118 (ptmt) cc_final: 0.8833 (ptmm) REVERT: TC 246 LYS cc_start: 0.8539 (mptp) cc_final: 0.8271 (mmtm) REVERT: TC 251 GLU cc_start: 0.9495 (mt-10) cc_final: 0.9154 (mt-10) REVERT: TC 352 CYS cc_start: 0.8786 (t) cc_final: 0.8379 (t) REVERT: TC 362 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8665 (mp0) REVERT: TC 363 GLN cc_start: 0.9156 (tp40) cc_final: 0.8413 (tp40) REVERT: TC 367 ASP cc_start: 0.9141 (m-30) cc_final: 0.8077 (m-30) REVERT: TC 372 ASN cc_start: 0.9072 (m-40) cc_final: 0.8243 (p0) REVERT: TC 407 MET cc_start: 0.9376 (mpp) cc_final: 0.9016 (mpp) REVERT: TC 411 ASN cc_start: 0.9261 (m-40) cc_final: 0.8630 (m-40) REVERT: TD 39 GLU cc_start: 0.9004 (tt0) cc_final: 0.8720 (tt0) REVERT: TD 58 ASP cc_start: 0.9063 (t70) cc_final: 0.8559 (t70) REVERT: TD 61 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8518 (mt-10) REVERT: TD 83 GLN cc_start: 0.9154 (mt0) cc_final: 0.8689 (tt0) REVERT: TD 85 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8670 (mt-10) REVERT: TE 58 ASP cc_start: 0.8923 (t70) cc_final: 0.8446 (t70) REVERT: TF 83 GLN cc_start: 0.8797 (mt0) cc_final: 0.8172 (tt0) REVERT: TG 58 ASP cc_start: 0.9078 (t70) cc_final: 0.8806 (t0) REVERT: TG 71 ASP cc_start: 0.9151 (t0) cc_final: 0.8665 (t0) REVERT: TG 83 GLN cc_start: 0.9217 (mt0) cc_final: 0.8921 (tt0) REVERT: TH 58 ASP cc_start: 0.8995 (t70) cc_final: 0.8601 (t0) REVERT: TH 83 GLN cc_start: 0.9030 (mt0) cc_final: 0.8681 (mt0) REVERT: TH 85 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8942 (mt-10) REVERT: TH 92 THR cc_start: 0.9633 (m) cc_final: 0.9394 (p) REVERT: TI 11 SER cc_start: 0.9167 (m) cc_final: 0.8863 (t) REVERT: TA 48 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9310 (mm) REVERT: TA 131 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8494 (mppt) REVERT: TA 155 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8712 (tp30) REVERT: TA 194 ASP cc_start: 0.8398 (t70) cc_final: 0.7451 (t0) REVERT: TA 222 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: TA 251 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8794 (mt-10) REVERT: TA 280 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8772 (mt-10) REVERT: TA 360 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8948 (tp30) REVERT: TA 367 ASP cc_start: 0.9094 (m-30) cc_final: 0.8877 (m-30) REVERT: TA 389 MET cc_start: 0.9121 (mtt) cc_final: 0.8683 (mtm) REVERT: TB 22 SER cc_start: 0.9349 (t) cc_final: 0.8877 (p) REVERT: TB 65 TRP cc_start: 0.8365 (m-90) cc_final: 0.7930 (m-90) REVERT: TB 131 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8024 (mptt) REVERT: TB 133 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6877 (mtm180) REVERT: TB 138 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8569 (p0) REVERT: TB 171 ASP cc_start: 0.9428 (t0) cc_final: 0.9148 (t0) REVERT: TB 246 LYS cc_start: 0.9086 (mptp) cc_final: 0.8632 (mmtt) REVERT: TB 251 GLU cc_start: 0.9327 (pt0) cc_final: 0.9039 (pm20) REVERT: TB 254 ASP cc_start: 0.9428 (m-30) cc_final: 0.9160 (m-30) REVERT: TB 272 ASP cc_start: 0.8557 (p0) cc_final: 0.7939 (p0) REVERT: TB 283 ASP cc_start: 0.8597 (p0) cc_final: 0.8319 (p0) REVERT: TB 362 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8377 (mm-30) REVERT: LA 192 MET cc_start: 0.9398 (tpt) cc_final: 0.7839 (mtt) REVERT: LA 253 LYS cc_start: 0.9162 (tttp) cc_final: 0.8949 (ttpp) REVERT: LA 281 ASN cc_start: 0.8215 (t0) cc_final: 0.7968 (t0) REVERT: LA 337 ASP cc_start: 0.9059 (m-30) cc_final: 0.8804 (m-30) REVERT: LA 361 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8154 (tp30) REVERT: LA 363 LYS cc_start: 0.8981 (mttt) cc_final: 0.8501 (mtpp) REVERT: LB 119 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8828 (pm20) REVERT: LB 126 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8352 (pm20) REVERT: LB 164 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7507 (mm-30) REVERT: LB 192 MET cc_start: 0.9485 (tpt) cc_final: 0.7434 (mtt) REVERT: LB 202 GLU cc_start: 0.9042 (tp30) cc_final: 0.8514 (tp30) REVERT: LF 153 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8560 (mt-10) REVERT: LF 192 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5160 (mpt) REVERT: LF 202 GLU cc_start: 0.9066 (tt0) cc_final: 0.8389 (tp30) REVERT: LF 206 GLN cc_start: 0.9310 (mm-40) cc_final: 0.8747 (mm110) REVERT: LF 337 ASP cc_start: 0.9230 (m-30) cc_final: 0.8770 (m-30) REVERT: LF 361 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: LE 192 MET cc_start: 0.8862 (tpt) cc_final: 0.7177 (mtt) REVERT: LE 317 ASP cc_start: 0.8928 (p0) cc_final: 0.8710 (p0) REVERT: LD 105 ASP cc_start: 0.8471 (m-30) cc_final: 0.7733 (t0) REVERT: LD 192 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.6744 (mtt) REVERT: LD 361 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: LD 367 ASP cc_start: 0.8998 (t0) cc_final: 0.8708 (t0) REVERT: LC 122 MET cc_start: 0.9525 (mmm) cc_final: 0.9313 (mmp) REVERT: LC 171 THR cc_start: 0.9212 (m) cc_final: 0.8873 (p) REVERT: LC 192 MET cc_start: 0.9308 (tpt) cc_final: 0.7500 (mtt) REVERT: LC 197 MET cc_start: 0.9010 (mmm) cc_final: 0.8303 (mpt) REVERT: LC 270 GLN cc_start: 0.9040 (pp30) cc_final: 0.8718 (pp30) REVERT: LC 358 GLN cc_start: 0.8917 (tt0) cc_final: 0.8389 (pm20) REVERT: LC 366 GLU cc_start: 0.9058 (mp0) cc_final: 0.8807 (mm-30) outliers start: 64 outliers final: 47 residues processed: 545 average time/residue: 0.6117 time to fit residues: 390.2558 Evaluate side-chains 545 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 489 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 128 THR Chi-restraints excluded: chain TC residue 172 VAL Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 7 ASN Chi-restraints excluded: chain TF residue 55 THR Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 54 LEU Chi-restraints excluded: chain TH residue 84 ILE Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 48 LEU Chi-restraints excluded: chain TA residue 85 SER Chi-restraints excluded: chain TA residue 124 SER Chi-restraints excluded: chain TA residue 128 THR Chi-restraints excluded: chain TA residue 138 ASN Chi-restraints excluded: chain TA residue 155 GLU Chi-restraints excluded: chain TA residue 178 MET Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 92 SER Chi-restraints excluded: chain TB residue 100 SER Chi-restraints excluded: chain TB residue 128 THR Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 138 ASN Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LA residue 381 VAL Chi-restraints excluded: chain LF residue 186 SER Chi-restraints excluded: chain LF residue 192 MET Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LF residue 381 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 201 ILE Chi-restraints excluded: chain LE residue 301 ILE Chi-restraints excluded: chain LE residue 356 ASN Chi-restraints excluded: chain LE residue 381 VAL Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 301 ILE Chi-restraints excluded: chain LD residue 306 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 175 VAL Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 293 GLU Chi-restraints excluded: chain LC residue 345 ARG Chi-restraints excluded: chain LC residue 360 VAL Chi-restraints excluded: chain LC residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 135 optimal weight: 9.9990 chunk 271 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 105 GLN ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN TG 31 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 83 GLN TA 394 GLN TB 138 ASN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 376 ASN LE 356 ASN LE 376 ASN ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066767 restraints weight = 51228.396| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.40 r_work: 0.2658 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28662 Z= 0.177 Angle : 0.589 13.113 38989 Z= 0.315 Chirality : 0.046 0.214 4385 Planarity : 0.003 0.045 5287 Dihedral : 5.780 65.211 4028 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 20.77 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.14), residues: 3635 helix: 1.53 (0.19), residues: 728 sheet: 0.10 (0.16), residues: 1022 loop : -0.67 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLB 193 TYR 0.026 0.002 TYRTC 290 PHE 0.016 0.001 PHETA 354 TRP 0.026 0.002 TRPTB 65 HIS 0.005 0.001 HISLE 349 Details of bonding type rmsd covalent geometry : bond 0.00396 (28656) covalent geometry : angle 0.58940 (38989) hydrogen bonds : bond 0.03797 ( 820) hydrogen bonds : angle 5.39969 ( 2304) metal coordination : bond 0.00109 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11260.02 seconds wall clock time: 191 minutes 53.89 seconds (11513.89 seconds total)