Starting phenix.real_space_refine on Tue Jun 24 09:06:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpq_18559/06_2025/8qpq_18559.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpq_18559/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpq_18559/06_2025/8qpq_18559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpq_18559/06_2025/8qpq_18559.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpq_18559/06_2025/8qpq_18559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpq_18559/06_2025/8qpq_18559.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.92, per 1000 atoms: 0.60 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: 7.07 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 3.25 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: 9.48 Time building geometry restraints manager: 8.31 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 396 or resid 401 through 405)) selection = (chain 'LB' and (resid 114 through 396 or resid 401 through 405)) selection = (chain 'LC' and (resid 114 through 396 or resid 401 through 405)) selection = (chain 'LD' and (resid 114 through 396 or resid 401 through 405)) selection = (chain 'LE' and (resid 114 through 396 or resid 401 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: 0.010 Normalize map: mean=0, sd=1: 1.260 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: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 68.800 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.077 0.018 TRPTA 156 HIS 0.046 0.005 HISLB 349 PHE 0.057 0.010 PHETB 354 TYR 0.105 0.016 TYRLE 267 ARG 0.043 0.005 ARGLC 389 Details of bonding type rmsd hydrogen bonds : bond 0.14483 ( 820) hydrogen bonds : angle 7.30501 ( 2304) metal coordination : bond 0.41573 ( 6) covalent geometry : bond 0.00933 (28656) covalent geometry : angle 1.59799 (38989) *********************** 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 : 2.857 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: 1.1965 time to fit residues: 1325.2707 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 : 3.005 ------------------------------------------------------------------------------- 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 305 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 328 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 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 TI 83 GLN TA 47 GLN TA 68 ASN TA 183 ASN ** TA 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TB 47 GLN TB 138 ASN TB 183 ASN TB 301 ASN TB 303 ASN TB 324 HIS LA 376 ASN LA 395 GLN ** LB 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 242 GLN LE 376 ASN LD 206 GLN 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: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.067001 restraints weight = 50573.035| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.38 r_work: 0.2654 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28662 Z= 0.188 Angle : 0.614 8.663 38989 Z= 0.338 Chirality : 0.048 0.303 4385 Planarity : 0.004 0.043 5287 Dihedral : 6.819 58.809 4040 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.25 % Allowed : 12.62 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3635 helix: 1.22 (0.19), residues: 741 sheet: 0.39 (0.15), residues: 1031 loop : -0.53 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLF 177 HIS 0.008 0.001 HISLE 349 PHE 0.025 0.002 PHETA 354 TYR 0.028 0.002 TYRTC 290 ARG 0.008 0.001 ARGLE 257 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 820) hydrogen bonds : angle 5.72695 ( 2304) metal coordination : bond 0.00161 ( 6) covalent geometry : bond 0.00419 (28656) covalent geometry : angle 0.61433 (38989) *********************** 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 727 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 628 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8740 (t0) cc_final: 0.8383 (t70) REVERT: TC 19 SER cc_start: 0.9032 (t) cc_final: 0.8806 (p) REVERT: TC 22 SER cc_start: 0.9038 (t) cc_final: 0.8650 (m) REVERT: TC 105 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8701 (mm-40) REVERT: TC 114 MET cc_start: 0.8738 (ttp) cc_final: 0.8433 (tmm) REVERT: TC 120 ASP cc_start: 0.8787 (t0) cc_final: 0.8545 (t0) REVERT: TC 131 LYS cc_start: 0.8370 (mppt) cc_final: 0.8153 (mtmt) REVERT: TC 142 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8340 (ttm-80) REVERT: TC 171 ASP cc_start: 0.9252 (t0) cc_final: 0.8607 (p0) REVERT: TC 194 ASP cc_start: 0.7721 (t0) cc_final: 0.6907 (t0) REVERT: TC 251 GLU cc_start: 0.9444 (mt-10) cc_final: 0.8884 (mt-10) REVERT: TC 326 MET cc_start: 0.9177 (ttm) cc_final: 0.8949 (ttm) REVERT: TC 352 CYS cc_start: 0.8618 (t) cc_final: 0.8227 (t) REVERT: TC 407 MET cc_start: 0.9298 (mpp) cc_final: 0.9006 (mpp) REVERT: TC 411 ASN cc_start: 0.9302 (m-40) cc_final: 0.8777 (m-40) REVERT: TD 39 GLU cc_start: 0.8934 (tt0) cc_final: 0.8601 (tt0) REVERT: TD 58 ASP cc_start: 0.8784 (t70) cc_final: 0.8345 (t70) REVERT: TD 83 GLN cc_start: 0.9023 (mt0) cc_final: 0.8392 (tt0) REVERT: TD 85 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8574 (mt-10) REVERT: TD 88 ASP cc_start: 0.8836 (t0) cc_final: 0.8610 (t0) REVERT: TD 92 THR cc_start: 0.9639 (m) cc_final: 0.9241 (p) REVERT: TE 9 GLN cc_start: 0.9291 (tp40) cc_final: 0.8959 (tp-100) REVERT: TE 58 ASP cc_start: 0.8803 (t70) cc_final: 0.8248 (t70) REVERT: TE 83 GLN cc_start: 0.9098 (tt0) cc_final: 0.8781 (tt0) REVERT: TE 85 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8776 (mt-10) REVERT: TF 7 ASN cc_start: 0.9109 (m-40) cc_final: 0.8805 (m110) REVERT: TF 9 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9034 (mm-40) REVERT: TF 39 GLU cc_start: 0.8775 (tt0) cc_final: 0.8134 (tt0) REVERT: TF 58 ASP cc_start: 0.8768 (t70) cc_final: 0.8550 (t70) REVERT: TF 83 GLN cc_start: 0.8882 (mt0) cc_final: 0.8622 (tt0) REVERT: TF 92 THR cc_start: 0.9711 (m) cc_final: 0.9024 (p) REVERT: TG 7 ASN cc_start: 0.8992 (m-40) cc_final: 0.8641 (m-40) REVERT: TG 29 ASP cc_start: 0.8850 (t0) cc_final: 0.8586 (t0) REVERT: TG 32 ASP cc_start: 0.9153 (m-30) cc_final: 0.8906 (m-30) REVERT: TG 58 ASP cc_start: 0.8951 (t70) cc_final: 0.8369 (t0) REVERT: TG 71 ASP cc_start: 0.9214 (t0) cc_final: 0.8674 (t0) REVERT: TG 92 THR cc_start: 0.9621 (m) cc_final: 0.9261 (p) REVERT: TG 93 TYR cc_start: 0.9121 (m-80) cc_final: 0.8775 (m-80) REVERT: TG 105 ASP cc_start: 0.9128 (m-30) cc_final: 0.8680 (m-30) REVERT: TH 7 ASN cc_start: 0.8775 (m110) cc_final: 0.8527 (m110) REVERT: TH 29 ASP cc_start: 0.9334 (t0) cc_final: 0.9109 (t70) REVERT: TH 39 GLU cc_start: 0.8889 (tt0) cc_final: 0.8616 (tt0) REVERT: TH 58 ASP cc_start: 0.8691 (t70) cc_final: 0.8383 (t70) REVERT: TH 76 GLU cc_start: 0.9014 (tt0) cc_final: 0.8784 (tt0) REVERT: TH 83 GLN cc_start: 0.9033 (mt0) cc_final: 0.8580 (mt0) REVERT: TH 85 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8906 (mt-10) REVERT: TH 92 THR cc_start: 0.9645 (m) cc_final: 0.9357 (p) REVERT: TI 83 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: TA 22 SER cc_start: 0.8903 (t) cc_final: 0.8483 (m) REVERT: TA 194 ASP cc_start: 0.8311 (t70) cc_final: 0.7266 (t0) REVERT: TA 222 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8279 (tp30) REVERT: TA 251 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8802 (mt-10) REVERT: TA 360 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8678 (mm-30) REVERT: TA 363 GLN cc_start: 0.9043 (tp40) cc_final: 0.8394 (tp40) REVERT: TA 366 ASN cc_start: 0.9423 (m-40) cc_final: 0.9188 (m110) REVERT: TA 367 ASP cc_start: 0.9310 (m-30) cc_final: 0.8482 (m-30) REVERT: TA 371 TYR cc_start: 0.8911 (m-80) cc_final: 0.8702 (m-10) REVERT: TA 372 ASN cc_start: 0.9161 (m-40) cc_final: 0.8755 (m-40) REVERT: TA 389 MET cc_start: 0.9233 (mtt) cc_final: 0.8899 (mtm) REVERT: TB 22 SER cc_start: 0.9335 (t) cc_final: 0.8831 (p) REVERT: TB 65 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7979 (m-90) REVERT: TB 81 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.7799 (t) REVERT: TB 97 ILE cc_start: 0.9337 (pt) cc_final: 0.8900 (mm) REVERT: TB 98 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8279 (ptp-110) REVERT: TB 120 ASP cc_start: 0.8802 (t0) cc_final: 0.8055 (p0) REVERT: TB 133 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6454 (mtm180) REVERT: TB 138 ASN cc_start: 0.8781 (t160) cc_final: 0.8529 (t0) REVERT: TB 171 ASP cc_start: 0.9367 (t0) cc_final: 0.8614 (p0) REVERT: TB 217 ASP cc_start: 0.9226 (m-30) cc_final: 0.8822 (m-30) REVERT: TB 222 GLU cc_start: 0.9103 (tt0) cc_final: 0.8753 (tm-30) REVERT: TB 229 ILE cc_start: 0.9524 (mp) cc_final: 0.9183 (tp) REVERT: TB 246 LYS cc_start: 0.9042 (mttp) cc_final: 0.8614 (mttt) REVERT: TB 251 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8866 (mt-10) REVERT: TB 254 ASP cc_start: 0.9415 (m-30) cc_final: 0.9193 (m-30) REVERT: TB 272 ASP cc_start: 0.8560 (p0) cc_final: 0.7858 (p0) REVERT: TB 315 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8828 (mp0) REVERT: TB 343 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9127 (mm) REVERT: TB 347 TRP cc_start: 0.9119 (m100) cc_final: 0.8726 (m100) REVERT: TB 362 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8284 (mm-30) REVERT: TB 389 MET cc_start: 0.9178 (mtt) cc_final: 0.8978 (mtp) REVERT: LA 120 VAL cc_start: 0.9119 (t) cc_final: 0.8882 (m) REVERT: LA 126 GLU cc_start: 0.8366 (pp20) cc_final: 0.8128 (pp20) REVERT: LA 192 MET cc_start: 0.9354 (tpt) cc_final: 0.7958 (tpp) REVERT: LA 202 GLU cc_start: 0.8937 (tt0) cc_final: 0.8563 (tp30) REVERT: LA 363 LYS cc_start: 0.8971 (mttt) cc_final: 0.8506 (mtpm) REVERT: LA 379 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8880 (tp) REVERT: LB 126 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8166 (pm20) REVERT: LB 167 ASP cc_start: 0.7454 (p0) cc_final: 0.7197 (m-30) REVERT: LB 192 MET cc_start: 0.9471 (tpt) cc_final: 0.7628 (mtt) REVERT: LB 293 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: LB 363 LYS cc_start: 0.9442 (mttt) cc_final: 0.9205 (mttt) REVERT: LF 133 GLU cc_start: 0.8887 (tp30) cc_final: 0.8592 (mp0) REVERT: LF 192 MET cc_start: 0.7857 (ttp) cc_final: 0.6925 (mmt) REVERT: LF 195 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8060 (mt0) REVERT: LF 202 GLU cc_start: 0.8991 (tt0) cc_final: 0.8551 (tm-30) REVERT: LF 206 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8905 (mm110) REVERT: LF 337 ASP cc_start: 0.9128 (m-30) cc_final: 0.8636 (m-30) REVERT: LF 361 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: LF 370 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.6565 (tpm-80) REVERT: LE 105 ASP cc_start: 0.8800 (t70) cc_final: 0.8600 (t0) REVERT: LE 122 MET cc_start: 0.9436 (mmt) cc_final: 0.9040 (mmm) REVERT: LE 133 GLU cc_start: 0.8222 (mp0) cc_final: 0.7902 (mp0) REVERT: LE 192 MET cc_start: 0.8857 (tpt) cc_final: 0.7241 (mtt) REVERT: LD 105 ASP cc_start: 0.8141 (m-30) cc_final: 0.7711 (t0) REVERT: LD 120 VAL cc_start: 0.9071 (t) cc_final: 0.8691 (p) REVERT: LD 192 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6892 (mtt) REVERT: LD 253 LYS cc_start: 0.9339 (ttpt) cc_final: 0.9119 (ttmt) REVERT: LD 361 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8853 (tt0) REVERT: LC 171 THR cc_start: 0.8997 (m) cc_final: 0.8653 (p) REVERT: LC 192 MET cc_start: 0.9260 (tpt) cc_final: 0.7520 (mtt) REVERT: LC 197 MET cc_start: 0.9106 (mmm) cc_final: 0.8076 (mpt) REVERT: LC 257 ARG cc_start: 0.8953 (tpp80) cc_final: 0.8552 (tpp80) REVERT: LC 290 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8483 (mtm-85) outliers start: 99 outliers final: 28 residues processed: 686 average time/residue: 1.3248 time to fit residues: 1069.4590 Evaluate side-chains 589 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 549 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 THR Chi-restraints excluded: chain TD residue 26 LEU Chi-restraints excluded: chain TE residue 78 ILE 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 TB residue 65 TRP 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 244 SER Chi-restraints excluded: chain TB residue 343 LEU 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 262 VAL Chi-restraints excluded: chain LB residue 293 GLU Chi-restraints excluded: chain LF residue 117 LEU Chi-restraints excluded: chain LF residue 361 GLU Chi-restraints excluded: chain LE residue 147 VAL Chi-restraints excluded: chain LE residue 171 THR 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 301 ILE Chi-restraints excluded: chain LD residue 361 GLU 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 237 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 158 optimal weight: 30.0000 chunk 290 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 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 342 GLN ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN TF 31 GLN TG 31 GLN TI 80 GLN TI 83 GLN TA 140 ASN TA 260 HIS TA 324 HIS TB 138 ASN TB 140 ASN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 356 ASN LA 376 ASN LB 238 ASN LB 270 GLN ** LB 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 356 ASN LF 229 GLN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 227 ASN LE 356 ASN LE 376 ASN LD 227 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.064672 restraints weight = 51268.689| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.37 r_work: 0.2603 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2771 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= 0.323 Angle : 0.631 8.184 38989 Z= 0.343 Chirality : 0.049 0.276 4385 Planarity : 0.004 0.043 5287 Dihedral : 6.358 60.114 4033 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.29 % Allowed : 13.97 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 3635 helix: 1.34 (0.19), residues: 735 sheet: 0.28 (0.15), residues: 1025 loop : -0.62 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLB 177 HIS 0.008 0.001 HISLE 349 PHE 0.023 0.002 PHETA 354 TYR 0.027 0.002 TYRTC 290 ARG 0.008 0.001 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 820) hydrogen bonds : angle 5.57189 ( 2304) metal coordination : bond 0.00358 ( 6) covalent geometry : bond 0.00716 (28656) covalent geometry : angle 0.63140 (38989) *********************** 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 640 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 540 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8605 (t0) cc_final: 0.8388 (t70) REVERT: TC 22 SER cc_start: 0.9149 (t) cc_final: 0.8686 (m) REVERT: TC 120 ASP cc_start: 0.8970 (t0) cc_final: 0.8732 (t0) REVERT: TC 142 ARG cc_start: 0.8769 (ttm170) cc_final: 0.8433 (ttm-80) REVERT: TC 178 MET cc_start: 0.9368 (ptm) cc_final: 0.8874 (pmm) REVERT: TC 194 ASP cc_start: 0.7666 (t0) cc_final: 0.6841 (t0) REVERT: TC 251 GLU cc_start: 0.9473 (mt-10) cc_final: 0.8983 (mt-10) REVERT: TC 256 LEU cc_start: 0.9531 (mt) cc_final: 0.9255 (mm) REVERT: TC 326 MET cc_start: 0.9236 (ttm) cc_final: 0.9003 (ttm) REVERT: TC 352 CYS cc_start: 0.8649 (t) cc_final: 0.8257 (t) REVERT: TC 407 MET cc_start: 0.9344 (mpp) cc_final: 0.8942 (mpp) REVERT: TC 411 ASN cc_start: 0.9319 (m-40) cc_final: 0.8759 (m-40) REVERT: TD 39 GLU cc_start: 0.8934 (tt0) cc_final: 0.8523 (tt0) REVERT: TD 58 ASP cc_start: 0.8902 (t70) cc_final: 0.8474 (t0) REVERT: TD 83 GLN cc_start: 0.9100 (mt0) cc_final: 0.8528 (tt0) REVERT: TD 85 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8591 (mt-10) REVERT: TD 88 ASP cc_start: 0.9069 (t0) cc_final: 0.8820 (t0) REVERT: TE 9 GLN cc_start: 0.9312 (tp40) cc_final: 0.8956 (tp-100) REVERT: TE 58 ASP cc_start: 0.8890 (t70) cc_final: 0.8500 (t70) REVERT: TE 83 GLN cc_start: 0.9205 (tt0) cc_final: 0.8969 (tt0) REVERT: TE 85 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8667 (mt-10) REVERT: TF 7 ASN cc_start: 0.9105 (m-40) cc_final: 0.8781 (m110) REVERT: TF 39 GLU cc_start: 0.8968 (tt0) cc_final: 0.8417 (tt0) REVERT: TF 58 ASP cc_start: 0.8853 (t70) cc_final: 0.8630 (t70) REVERT: TF 83 GLN cc_start: 0.9038 (mt0) cc_final: 0.8650 (tt0) REVERT: TF 92 THR cc_start: 0.9722 (m) cc_final: 0.9104 (p) REVERT: TG 7 ASN cc_start: 0.8997 (m-40) cc_final: 0.8656 (m-40) REVERT: TG 83 GLN cc_start: 0.9201 (mt0) cc_final: 0.8855 (tt0) REVERT: TG 92 THR cc_start: 0.9595 (m) cc_final: 0.9254 (p) REVERT: TG 93 TYR cc_start: 0.9248 (m-80) cc_final: 0.8885 (m-80) REVERT: TH 29 ASP cc_start: 0.9353 (t0) cc_final: 0.9130 (t70) REVERT: TH 58 ASP cc_start: 0.8812 (t70) cc_final: 0.8571 (t70) REVERT: TH 76 GLU cc_start: 0.9019 (tt0) cc_final: 0.8800 (tt0) REVERT: TH 83 GLN cc_start: 0.9056 (mt0) cc_final: 0.8666 (mt0) REVERT: TH 85 GLU cc_start: 0.9419 (mt-10) cc_final: 0.8848 (mt-10) REVERT: TH 92 THR cc_start: 0.9643 (m) cc_final: 0.9277 (p) REVERT: TA 22 SER cc_start: 0.8979 (t) cc_final: 0.8540 (m) REVERT: TA 155 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8770 (tp30) REVERT: TA 194 ASP cc_start: 0.8380 (t70) cc_final: 0.7365 (t0) REVERT: TA 222 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: TA 251 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8802 (mt-10) REVERT: TA 360 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8839 (tp30) REVERT: TA 363 GLN cc_start: 0.9095 (tp40) cc_final: 0.8861 (tp40) REVERT: TA 367 ASP cc_start: 0.9275 (m-30) cc_final: 0.8965 (m-30) REVERT: TA 371 TYR cc_start: 0.8945 (m-80) cc_final: 0.8743 (m-10) REVERT: TA 372 ASN cc_start: 0.9156 (m-40) cc_final: 0.8770 (m-40) REVERT: TA 389 MET cc_start: 0.9216 (mtt) cc_final: 0.8887 (mtm) REVERT: TB 22 SER cc_start: 0.9345 (t) cc_final: 0.8883 (p) REVERT: TB 97 ILE cc_start: 0.9342 (pt) cc_final: 0.9098 (mt) REVERT: TB 98 ARG cc_start: 0.8530 (ptp-170) cc_final: 0.8260 (ptp90) REVERT: TB 131 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7863 (mptt) REVERT: TB 133 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6449 (mtm180) REVERT: TB 138 ASN cc_start: 0.8928 (t0) cc_final: 0.8668 (t0) REVERT: TB 171 ASP cc_start: 0.9405 (t0) cc_final: 0.8608 (p0) REVERT: TB 194 ASP cc_start: 0.8528 (m-30) cc_final: 0.7772 (m-30) REVERT: TB 222 GLU cc_start: 0.9100 (tt0) cc_final: 0.8745 (tp30) REVERT: TB 238 LYS cc_start: 0.9114 (ttpp) cc_final: 0.8727 (ttpp) REVERT: TB 251 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8732 (mt-10) REVERT: TB 272 ASP cc_start: 0.8615 (p0) cc_final: 0.7928 (p0) REVERT: TB 283 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8391 (p0) REVERT: TB 289 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8995 (tttt) REVERT: TB 315 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8960 (mt-10) REVERT: TB 362 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8305 (mm-30) REVERT: LA 120 VAL cc_start: 0.9203 (t) cc_final: 0.8970 (m) REVERT: LA 181 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8641 (ttpt) REVERT: LA 192 MET cc_start: 0.9380 (tpt) cc_final: 0.7942 (tpp) REVERT: LA 281 ASN cc_start: 0.8498 (t0) cc_final: 0.8237 (t0) REVERT: LA 337 ASP cc_start: 0.9166 (m-30) cc_final: 0.8801 (m-30) REVERT: LA 363 LYS cc_start: 0.8915 (mttt) cc_final: 0.8421 (mtpm) REVERT: LA 378 ARG cc_start: 0.9199 (ptp90) cc_final: 0.8974 (ptp-110) REVERT: LB 125 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8959 (ptt90) REVERT: LB 126 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8306 (pm20) REVERT: LB 192 MET cc_start: 0.9472 (tpt) cc_final: 0.7508 (mtt) REVERT: LB 293 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8605 (pt0) REVERT: LF 192 MET cc_start: 0.6904 (ttp) cc_final: 0.5911 (mmt) REVERT: LF 202 GLU cc_start: 0.9048 (tt0) cc_final: 0.8393 (tp30) REVERT: LF 206 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8811 (mm-40) REVERT: LF 337 ASP cc_start: 0.9202 (m-30) cc_final: 0.8722 (m-30) REVERT: LF 361 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: LE 105 ASP cc_start: 0.8938 (t70) cc_final: 0.8732 (t0) REVERT: LE 133 GLU cc_start: 0.8272 (mp0) cc_final: 0.7974 (mp0) REVERT: LE 192 MET cc_start: 0.8878 (tpt) cc_final: 0.7222 (mtt) REVERT: LE 257 ARG cc_start: 0.8933 (tpp80) cc_final: 0.8724 (tpp80) REVERT: LE 361 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: LD 101 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.7925 (p90) REVERT: LD 105 ASP cc_start: 0.8309 (m-30) cc_final: 0.7698 (t0) REVERT: LD 120 VAL cc_start: 0.9196 (t) cc_final: 0.8867 (p) REVERT: LD 192 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7058 (mtt) REVERT: LD 253 LYS cc_start: 0.9369 (ttpt) cc_final: 0.9147 (ttmt) REVERT: LD 361 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8801 (tt0) REVERT: LC 120 VAL cc_start: 0.9387 (m) cc_final: 0.9180 (p) REVERT: LC 171 THR cc_start: 0.9126 (m) cc_final: 0.8772 (p) REVERT: LC 192 MET cc_start: 0.9317 (tpt) cc_final: 0.7530 (mtt) REVERT: LC 197 MET cc_start: 0.9074 (mmm) cc_final: 0.8190 (mpt) REVERT: LC 257 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8656 (tpp80) REVERT: LC 290 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8395 (mtm-85) outliers start: 100 outliers final: 40 residues processed: 600 average time/residue: 1.7868 time to fit residues: 1252.2120 Evaluate side-chains 541 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 487 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 50 SER Chi-restraints excluded: chain TC residue 62 LEU Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 195 ILE Chi-restraints excluded: chain TD residue 26 LEU 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 TI residue 40 ILE Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 85 SER 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 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 177 THR Chi-restraints excluded: chain TB residue 244 SER Chi-restraints excluded: chain TB residue 283 ASP Chi-restraints excluded: chain TB residue 289 LYS Chi-restraints excluded: chain TB residue 339 THR Chi-restraints excluded: chain LA residue 181 LYS 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 LB residue 105 ASP Chi-restraints excluded: chain LB residue 125 ARG 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 LE residue 101 PHE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 290 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 349 ASN 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** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 83 GLN TB 260 HIS ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 356 ASN ** LB 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 376 ASN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 380 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.066089 restraints weight = 51368.416| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.40 r_work: 0.2640 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3040 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= 0.190 Angle : 0.552 8.555 38989 Z= 0.300 Chirality : 0.046 0.269 4385 Planarity : 0.003 0.044 5287 Dihedral : 6.069 64.728 4032 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.79 % Allowed : 15.51 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 3635 helix: 1.44 (0.19), residues: 745 sheet: 0.28 (0.15), residues: 1019 loop : -0.62 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPTB 65 HIS 0.006 0.001 HISLE 349 PHE 0.020 0.001 PHETA 354 TYR 0.026 0.002 TYRTC 290 ARG 0.008 0.001 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 820) hydrogen bonds : angle 5.35425 ( 2304) metal coordination : bond 0.00148 ( 6) covalent geometry : bond 0.00422 (28656) covalent geometry : angle 0.55214 (38989) *********************** 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 649 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 564 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8606 (t0) cc_final: 0.8224 (t70) REVERT: TC 22 SER cc_start: 0.9040 (t) cc_final: 0.8621 (m) REVERT: TC 75 GLU cc_start: 0.8239 (tp30) cc_final: 0.7950 (tp30) REVERT: TC 120 ASP cc_start: 0.8946 (t0) cc_final: 0.8727 (t0) REVERT: TC 142 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8440 (ttp-170) REVERT: TC 194 ASP cc_start: 0.7826 (t0) cc_final: 0.7031 (t0) REVERT: TC 251 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9051 (mt-10) REVERT: TC 294 ASP cc_start: 0.8841 (m-30) cc_final: 0.8632 (m-30) REVERT: TC 326 MET cc_start: 0.9210 (ttm) cc_final: 0.9000 (ttm) REVERT: TC 352 CYS cc_start: 0.8615 (t) cc_final: 0.8155 (t) REVERT: TC 363 GLN cc_start: 0.9180 (tp40) cc_final: 0.8750 (tp40) REVERT: TC 372 ASN cc_start: 0.9185 (m-40) cc_final: 0.8122 (p0) REVERT: TC 400 ASP cc_start: 0.8706 (t70) cc_final: 0.8250 (p0) REVERT: TC 407 MET cc_start: 0.9364 (mpp) cc_final: 0.8994 (mpp) REVERT: TC 411 ASN cc_start: 0.9304 (m-40) cc_final: 0.8702 (m-40) REVERT: TD 39 GLU cc_start: 0.8909 (tt0) cc_final: 0.8514 (tt0) REVERT: TD 58 ASP cc_start: 0.8927 (t70) cc_final: 0.8468 (t0) REVERT: TD 83 GLN cc_start: 0.9075 (mt0) cc_final: 0.8555 (tt0) REVERT: TD 85 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8680 (mt-10) REVERT: TD 88 ASP cc_start: 0.9025 (t0) cc_final: 0.8789 (t0) REVERT: TE 58 ASP cc_start: 0.8921 (t70) cc_final: 0.8528 (t70) REVERT: TE 83 GLN cc_start: 0.9092 (tt0) cc_final: 0.8822 (tt0) REVERT: TE 85 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8762 (mt-10) REVERT: TF 9 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8952 (mm-40) REVERT: TF 39 GLU cc_start: 0.8984 (tt0) cc_final: 0.8400 (tt0) REVERT: TF 58 ASP cc_start: 0.8895 (t70) cc_final: 0.8670 (t70) REVERT: TF 83 GLN cc_start: 0.8949 (mt0) cc_final: 0.8629 (tt0) REVERT: TF 92 THR cc_start: 0.9711 (m) cc_final: 0.9093 (p) REVERT: TG 7 ASN cc_start: 0.8935 (m-40) cc_final: 0.8588 (m-40) REVERT: TG 29 ASP cc_start: 0.8935 (t0) cc_final: 0.8707 (t0) REVERT: TG 71 ASP cc_start: 0.9141 (t0) cc_final: 0.8638 (t0) REVERT: TG 83 GLN cc_start: 0.9134 (mt0) cc_final: 0.8788 (tt0) REVERT: TG 92 THR cc_start: 0.9575 (m) cc_final: 0.9188 (p) REVERT: TG 93 TYR cc_start: 0.9239 (m-80) cc_final: 0.8964 (m-80) REVERT: TG 105 ASP cc_start: 0.9118 (m-30) cc_final: 0.8620 (m-30) REVERT: TH 29 ASP cc_start: 0.9384 (t0) cc_final: 0.9182 (t70) REVERT: TH 58 ASP cc_start: 0.8898 (t70) cc_final: 0.8598 (t70) REVERT: TH 83 GLN cc_start: 0.9030 (mt0) cc_final: 0.8578 (mt0) REVERT: TH 85 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8762 (mt-10) REVERT: TH 92 THR cc_start: 0.9643 (m) cc_final: 0.9363 (p) REVERT: TA 22 SER cc_start: 0.8905 (t) cc_final: 0.8485 (m) REVERT: TA 97 ILE cc_start: 0.9632 (pt) cc_final: 0.9372 (pp) REVERT: TA 131 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8623 (mppt) REVERT: TA 133 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7813 (pmm-80) REVERT: TA 155 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8740 (tp30) REVERT: TA 194 ASP cc_start: 0.8352 (t70) cc_final: 0.7356 (t0) REVERT: TA 222 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: TA 251 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8894 (mt-10) REVERT: TA 280 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8719 (mt-10) REVERT: TA 315 GLU cc_start: 0.8802 (mp0) cc_final: 0.8557 (pm20) REVERT: TA 360 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8876 (tp30) REVERT: TA 367 ASP cc_start: 0.9294 (m-30) cc_final: 0.9012 (m-30) REVERT: TA 372 ASN cc_start: 0.9107 (m-40) cc_final: 0.8692 (m-40) REVERT: TA 389 MET cc_start: 0.9153 (mtt) cc_final: 0.8801 (mtm) REVERT: TB 22 SER cc_start: 0.9307 (t) cc_final: 0.8832 (p) REVERT: TB 65 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7771 (m-90) REVERT: TB 131 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7819 (mptt) REVERT: TB 133 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6688 (mtm180) REVERT: TB 138 ASN cc_start: 0.8904 (t0) cc_final: 0.8696 (t0) REVERT: TB 171 ASP cc_start: 0.9409 (t0) cc_final: 0.8685 (p0) REVERT: TB 178 MET cc_start: 0.9203 (ptm) cc_final: 0.8769 (ppp) REVERT: TB 194 ASP cc_start: 0.8516 (m-30) cc_final: 0.7871 (m-30) REVERT: TB 222 GLU cc_start: 0.9112 (tt0) cc_final: 0.8491 (tm-30) REVERT: TB 238 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8746 (ttpp) REVERT: TB 251 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8750 (mt-10) REVERT: TB 272 ASP cc_start: 0.8584 (p0) cc_final: 0.7870 (p0) REVERT: TB 362 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8429 (mm-30) REVERT: LA 120 VAL cc_start: 0.9212 (t) cc_final: 0.8982 (m) REVERT: LA 181 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8426 (ttpp) REVERT: LA 192 MET cc_start: 0.9381 (tpt) cc_final: 0.7896 (tpp) REVERT: LA 281 ASN cc_start: 0.8251 (t0) cc_final: 0.7884 (t0) REVERT: LA 337 ASP cc_start: 0.9121 (m-30) cc_final: 0.8866 (m-30) REVERT: LA 361 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8180 (tp30) REVERT: LA 363 LYS cc_start: 0.8953 (mttt) cc_final: 0.8380 (mtpp) REVERT: LA 378 ARG cc_start: 0.9219 (ptp90) cc_final: 0.8981 (ptp-110) REVERT: LB 119 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8851 (pm20) REVERT: LB 126 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8282 (pm20) REVERT: LB 192 MET cc_start: 0.9438 (tpt) cc_final: 0.7436 (mtt) REVERT: LF 192 MET cc_start: 0.6878 (ttp) cc_final: 0.5900 (mmt) REVERT: LF 202 GLU cc_start: 0.9039 (tt0) cc_final: 0.8435 (tm-30) REVERT: LF 206 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8786 (mm-40) REVERT: LF 337 ASP cc_start: 0.9160 (m-30) cc_final: 0.8695 (m-30) REVERT: LF 361 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: LE 105 ASP cc_start: 0.8868 (t70) cc_final: 0.8651 (t0) REVERT: LE 133 GLU cc_start: 0.8331 (mp0) cc_final: 0.8084 (mp0) REVERT: LE 192 MET cc_start: 0.8830 (tpt) cc_final: 0.7133 (mtt) REVERT: LE 337 ASP cc_start: 0.9156 (m-30) cc_final: 0.8879 (m-30) REVERT: LD 101 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7999 (p90) REVERT: LD 105 ASP cc_start: 0.8334 (m-30) cc_final: 0.7671 (t0) REVERT: LD 120 VAL cc_start: 0.9281 (t) cc_final: 0.9016 (p) REVERT: LD 192 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.6752 (mtt) REVERT: LD 253 LYS cc_start: 0.9347 (ttpt) cc_final: 0.9144 (ttmt) REVERT: LC 120 VAL cc_start: 0.9393 (m) cc_final: 0.9095 (p) REVERT: LC 171 THR cc_start: 0.9134 (m) cc_final: 0.8774 (p) REVERT: LC 192 MET cc_start: 0.9246 (tpt) cc_final: 0.7433 (mtt) REVERT: LC 197 MET cc_start: 0.9027 (mmm) cc_final: 0.8152 (mpt) REVERT: LC 257 ARG cc_start: 0.8951 (tpp80) cc_final: 0.8630 (tpp80) REVERT: LC 290 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8406 (mtm-85) outliers start: 85 outliers final: 26 residues processed: 618 average time/residue: 1.3200 time to fit residues: 959.5432 Evaluate side-chains 553 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 516 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 195 ILE Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 9 GLN 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 85 SER Chi-restraints excluded: chain TA residue 133 ARG 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 222 GLU Chi-restraints excluded: chain TB residue 65 TRP Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 181 LYS Chi-restraints excluded: chain LA residue 262 VAL Chi-restraints excluded: chain LA residue 333 SER Chi-restraints excluded: chain LB residue 121 VAL 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 101 PHE 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 101 PHE Chi-restraints excluded: chain LD residue 192 MET Chi-restraints excluded: chain LD residue 333 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 20 optimal weight: 40.0000 chunk 349 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 343 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 9 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 31 GLN TI 80 GLN TI 83 GLN TA 205 GLN TB 205 GLN ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 349 HIS ** 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 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 356 ASN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.091808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.064667 restraints weight = 51266.740| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.39 r_work: 0.2621 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 28662 Z= 0.265 Angle : 0.585 9.699 38989 Z= 0.315 Chirality : 0.047 0.278 4385 Planarity : 0.004 0.044 5287 Dihedral : 5.875 62.749 4027 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.25 % Allowed : 16.89 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 3635 helix: 1.60 (0.19), residues: 719 sheet: 0.15 (0.15), residues: 1052 loop : -0.64 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLB 177 HIS 0.007 0.001 HISLE 349 PHE 0.018 0.002 PHETA 354 TYR 0.027 0.002 TYRTC 290 ARG 0.008 0.001 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 820) hydrogen bonds : angle 5.40459 ( 2304) metal coordination : bond 0.00237 ( 6) covalent geometry : bond 0.00589 (28656) covalent geometry : angle 0.58536 (38989) *********************** 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 631 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 532 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8636 (t0) cc_final: 0.8413 (t70) REVERT: TC 22 SER cc_start: 0.9113 (t) cc_final: 0.8622 (m) REVERT: TC 120 ASP cc_start: 0.9052 (t0) cc_final: 0.8820 (t0) REVERT: TC 131 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7525 (mptt) REVERT: TC 142 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8438 (tpp-160) REVERT: TC 174 ASN cc_start: 0.8807 (t0) cc_final: 0.8581 (p0) REVERT: TC 194 ASP cc_start: 0.7734 (t0) cc_final: 0.7123 (t0) REVERT: TC 251 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9204 (mt-10) REVERT: TC 294 ASP cc_start: 0.8880 (m-30) cc_final: 0.8614 (m-30) REVERT: TC 326 MET cc_start: 0.9283 (ttm) cc_final: 0.9068 (ttm) REVERT: TC 352 CYS cc_start: 0.8704 (t) cc_final: 0.8259 (t) REVERT: TC 372 ASN cc_start: 0.9094 (m-40) cc_final: 0.8168 (p0) REVERT: TC 400 ASP cc_start: 0.8779 (t70) cc_final: 0.8261 (p0) REVERT: TC 407 MET cc_start: 0.9375 (mpp) cc_final: 0.8972 (mpp) REVERT: TC 411 ASN cc_start: 0.9284 (m-40) cc_final: 0.8659 (m-40) REVERT: TD 39 GLU cc_start: 0.8958 (tt0) cc_final: 0.8636 (tt0) REVERT: TD 58 ASP cc_start: 0.8993 (t70) cc_final: 0.8508 (t0) REVERT: TD 83 GLN cc_start: 0.9128 (mt0) cc_final: 0.8607 (tt0) REVERT: TD 85 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8607 (mt-10) REVERT: TE 58 ASP cc_start: 0.8908 (t70) cc_final: 0.8446 (t70) REVERT: TE 83 GLN cc_start: 0.9139 (tt0) cc_final: 0.8887 (tt0) REVERT: TE 85 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8744 (mt-10) REVERT: TF 9 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8936 (mm-40) REVERT: TF 58 ASP cc_start: 0.8891 (t70) cc_final: 0.8650 (t70) REVERT: TF 83 GLN cc_start: 0.9059 (mt0) cc_final: 0.8490 (tt0) REVERT: TF 92 THR cc_start: 0.9709 (m) cc_final: 0.9103 (p) REVERT: TG 71 ASP cc_start: 0.9146 (t0) cc_final: 0.8682 (t0) REVERT: TG 83 GLN cc_start: 0.9164 (mt0) cc_final: 0.8785 (tt0) REVERT: TG 93 TYR cc_start: 0.9256 (m-80) cc_final: 0.8939 (m-80) REVERT: TH 58 ASP cc_start: 0.8962 (t70) cc_final: 0.8627 (t70) REVERT: TH 83 GLN cc_start: 0.9013 (mt0) cc_final: 0.8612 (mt0) REVERT: TH 85 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8814 (mt-10) REVERT: TH 92 THR cc_start: 0.9641 (m) cc_final: 0.9369 (p) REVERT: TA 112 PHE cc_start: 0.8770 (m-80) cc_final: 0.8541 (m-80) REVERT: TA 131 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8732 (mppt) REVERT: TA 133 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7866 (pmm-80) REVERT: TA 143 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8872 (p) REVERT: TA 155 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8726 (tp30) REVERT: TA 171 ASP cc_start: 0.9060 (t0) cc_final: 0.8614 (t0) REVERT: TA 194 ASP cc_start: 0.8353 (t70) cc_final: 0.7342 (t0) REVERT: TA 222 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: TA 251 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8837 (mt-10) REVERT: TA 280 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8693 (mt-10) REVERT: TA 360 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8890 (tp30) REVERT: TA 367 ASP cc_start: 0.9165 (m-30) cc_final: 0.8813 (m-30) REVERT: TA 389 MET cc_start: 0.9173 (mtt) cc_final: 0.8809 (mtm) REVERT: TB 22 SER cc_start: 0.9341 (t) cc_final: 0.8875 (p) REVERT: TB 110 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8205 (mmmm) REVERT: TB 131 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7854 (mptt) REVERT: TB 133 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6747 (mtm180) REVERT: TB 138 ASN cc_start: 0.8958 (t0) cc_final: 0.8730 (t0) REVERT: TB 171 ASP cc_start: 0.9417 (t0) cc_final: 0.8679 (p0) REVERT: TB 194 ASP cc_start: 0.8593 (m-30) cc_final: 0.7866 (m-30) REVERT: TB 222 GLU cc_start: 0.9108 (tt0) cc_final: 0.8401 (tm-30) REVERT: TB 251 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8764 (mt-10) REVERT: TB 272 ASP cc_start: 0.8604 (p0) cc_final: 0.7948 (p0) REVERT: TB 362 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8434 (mm-30) REVERT: LA 120 VAL cc_start: 0.9232 (t) cc_final: 0.8992 (m) REVERT: LA 181 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8785 (ttpt) REVERT: LA 192 MET cc_start: 0.9390 (tpt) cc_final: 0.7924 (tpp) REVERT: LA 281 ASN cc_start: 0.8218 (t0) cc_final: 0.7833 (t0) REVERT: LA 337 ASP cc_start: 0.9056 (m-30) cc_final: 0.8805 (m-30) REVERT: LA 361 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8146 (tp30) REVERT: LA 363 LYS cc_start: 0.8922 (mttt) cc_final: 0.8405 (mtpp) REVERT: LA 378 ARG cc_start: 0.9207 (ptp90) cc_final: 0.8981 (ptp-110) REVERT: LB 107 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9079 (mt-10) REVERT: LB 119 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8855 (pm20) REVERT: LB 126 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8321 (pm20) REVERT: LB 192 MET cc_start: 0.9445 (tpt) cc_final: 0.7412 (mtt) REVERT: LF 117 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8918 (mm) REVERT: LF 192 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5813 (mpt) REVERT: LF 202 GLU cc_start: 0.9061 (tt0) cc_final: 0.8455 (tm-30) REVERT: LF 206 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8794 (mm-40) REVERT: LF 337 ASP cc_start: 0.9205 (m-30) cc_final: 0.8612 (m-30) REVERT: LF 361 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: LF 365 TYR cc_start: 0.9267 (p90) cc_final: 0.8721 (p90) REVERT: LE 105 ASP cc_start: 0.8871 (t70) cc_final: 0.8654 (t0) REVERT: LE 133 GLU cc_start: 0.8393 (mp0) cc_final: 0.8160 (mp0) REVERT: LE 192 MET cc_start: 0.8835 (tpt) cc_final: 0.7143 (mtt) REVERT: LE 337 ASP cc_start: 0.9181 (m-30) cc_final: 0.8899 (m-30) REVERT: LE 361 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: LD 101 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8040 (p90) REVERT: LD 105 ASP cc_start: 0.8384 (m-30) cc_final: 0.7692 (t0) REVERT: LD 120 VAL cc_start: 0.9310 (t) cc_final: 0.9059 (p) REVERT: LD 192 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.6845 (mtt) REVERT: LD 253 LYS cc_start: 0.9383 (ttpt) cc_final: 0.9164 (ttmt) REVERT: LD 356 ASN cc_start: 0.9208 (m-40) cc_final: 0.8956 (m110) REVERT: LD 361 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8808 (tt0) REVERT: LC 171 THR cc_start: 0.9154 (m) cc_final: 0.8821 (p) REVERT: LC 192 MET cc_start: 0.9274 (tpt) cc_final: 0.7454 (mtt) REVERT: LC 197 MET cc_start: 0.9003 (mmm) cc_final: 0.8157 (mpt) REVERT: LC 290 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8459 (mtm-85) outliers start: 99 outliers final: 35 residues processed: 591 average time/residue: 1.5771 time to fit residues: 1100.5234 Evaluate side-chains 559 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 508 time to evaluate : 5.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 103 THR Chi-restraints excluded: chain TC residue 195 ILE Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 9 GLN Chi-restraints excluded: chain TF residue 34 LYS 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 133 ARG 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 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 110 LYS Chi-restraints excluded: chain TB residue 133 ARG 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 367 ASP Chi-restraints excluded: chain LA residue 168 ASP Chi-restraints excluded: chain LA residue 181 LYS 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 121 VAL 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 192 MET Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LD residue 361 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 95 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 343 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 185 optimal weight: 30.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 260 HIS TD 31 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 395 GLN LE 136 ASN LE 356 ASN LE 376 ASN LE 380 HIS ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.070435 restraints weight = 51042.935| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.43 r_work: 0.2726 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28662 Z= 0.099 Angle : 0.519 9.000 38989 Z= 0.278 Chirality : 0.045 0.289 4385 Planarity : 0.003 0.046 5287 Dihedral : 5.721 70.753 4027 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 18.83 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3635 helix: 1.64 (0.19), residues: 740 sheet: 0.22 (0.16), residues: 1041 loop : -0.62 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPTB 65 HIS 0.003 0.001 HISLE 349 PHE 0.016 0.001 PHETA 354 TYR 0.026 0.001 TYRTC 290 ARG 0.010 0.000 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 820) hydrogen bonds : angle 5.18686 ( 2304) metal coordination : bond 0.00054 ( 6) covalent geometry : bond 0.00218 (28656) covalent geometry : angle 0.51914 (38989) *********************** 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 663 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 603 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8610 (t0) cc_final: 0.8156 (t70) REVERT: TC 22 SER cc_start: 0.9019 (t) cc_final: 0.8573 (m) REVERT: TC 65 TRP cc_start: 0.8078 (m-90) cc_final: 0.7829 (m-90) REVERT: TC 75 GLU cc_start: 0.8221 (tp30) cc_final: 0.7984 (tp30) REVERT: TC 80 TYR cc_start: 0.9294 (t80) cc_final: 0.8963 (t80) REVERT: TC 120 ASP cc_start: 0.8985 (t0) cc_final: 0.8708 (t0) REVERT: TC 131 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7741 (mptt) REVERT: TC 142 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8631 (ttp-170) REVERT: TC 171 ASP cc_start: 0.9316 (t0) cc_final: 0.9111 (t0) REVERT: TC 179 THR cc_start: 0.8499 (p) cc_final: 0.7902 (t) REVERT: TC 194 ASP cc_start: 0.7964 (t0) cc_final: 0.7002 (t0) REVERT: TC 247 LEU cc_start: 0.8495 (mp) cc_final: 0.8279 (mt) REVERT: TC 251 GLU cc_start: 0.9495 (mt-10) cc_final: 0.9248 (mt-10) REVERT: TC 260 HIS cc_start: 0.9186 (p-80) cc_final: 0.8859 (p-80) REVERT: TC 294 ASP cc_start: 0.8836 (m-30) cc_final: 0.8588 (m-30) REVERT: TC 352 CYS cc_start: 0.8616 (t) cc_final: 0.8149 (t) REVERT: TC 362 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8634 (mp0) REVERT: TC 363 GLN cc_start: 0.9184 (tp40) cc_final: 0.8402 (tp40) REVERT: TC 367 ASP cc_start: 0.9122 (m-30) cc_final: 0.8268 (m-30) REVERT: TC 372 ASN cc_start: 0.9056 (m-40) cc_final: 0.8293 (p0) REVERT: TC 400 ASP cc_start: 0.8743 (t70) cc_final: 0.8281 (p0) REVERT: TC 407 MET cc_start: 0.9338 (mpp) cc_final: 0.8976 (mpp) REVERT: TC 411 ASN cc_start: 0.9234 (m-40) cc_final: 0.8633 (m-40) REVERT: TD 39 GLU cc_start: 0.8876 (tt0) cc_final: 0.8538 (tt0) REVERT: TD 58 ASP cc_start: 0.8988 (t70) cc_final: 0.8492 (t0) REVERT: TD 83 GLN cc_start: 0.9018 (mt0) cc_final: 0.8579 (tt0) REVERT: TD 85 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8604 (mt-10) REVERT: TE 58 ASP cc_start: 0.8898 (t70) cc_final: 0.8463 (t70) REVERT: TE 83 GLN cc_start: 0.8980 (tt0) cc_final: 0.8712 (tt0) REVERT: TE 85 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8525 (mt-10) REVERT: TF 39 GLU cc_start: 0.8951 (tt0) cc_final: 0.8502 (tt0) REVERT: TF 58 ASP cc_start: 0.8925 (t70) cc_final: 0.8690 (t70) REVERT: TF 83 GLN cc_start: 0.8814 (mt0) cc_final: 0.8456 (tt0) REVERT: TF 92 THR cc_start: 0.9693 (m) cc_final: 0.9051 (p) REVERT: TG 58 ASP cc_start: 0.9038 (t70) cc_final: 0.8802 (t0) REVERT: TG 61 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8495 (mp0) REVERT: TG 64 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8741 (tm-30) REVERT: TG 71 ASP cc_start: 0.9148 (t0) cc_final: 0.8840 (t0) REVERT: TG 83 GLN cc_start: 0.9055 (mt0) cc_final: 0.8755 (tt0) REVERT: TG 105 ASP cc_start: 0.9077 (m-30) cc_final: 0.8605 (m-30) REVERT: TH 29 ASP cc_start: 0.9350 (t0) cc_final: 0.9129 (t70) REVERT: TH 52 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8600 (mt-10) REVERT: TH 58 ASP cc_start: 0.9018 (t70) cc_final: 0.8716 (t70) REVERT: TH 83 GLN cc_start: 0.8949 (mt0) cc_final: 0.8419 (tt0) REVERT: TH 85 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8916 (mt-10) REVERT: TH 92 THR cc_start: 0.9644 (m) cc_final: 0.9258 (p) REVERT: TI 52 GLU cc_start: 0.8838 (tt0) cc_final: 0.8415 (mt-10) REVERT: TA 97 ILE cc_start: 0.9608 (pt) cc_final: 0.9359 (pp) REVERT: TA 112 PHE cc_start: 0.8763 (m-80) cc_final: 0.8415 (m-80) REVERT: TA 131 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8559 (mppt) REVERT: TA 194 ASP cc_start: 0.8300 (t70) cc_final: 0.7314 (t0) REVERT: TA 222 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: TA 280 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8681 (mt-10) REVERT: TA 360 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8898 (tp30) REVERT: TA 389 MET cc_start: 0.9137 (mtt) cc_final: 0.8796 (mtm) REVERT: TB 22 SER cc_start: 0.9290 (t) cc_final: 0.8838 (p) REVERT: TB 138 ASN cc_start: 0.9006 (t0) cc_final: 0.8759 (t0) REVERT: TB 171 ASP cc_start: 0.9422 (t0) cc_final: 0.8687 (p0) REVERT: TB 178 MET cc_start: 0.9176 (ptm) cc_final: 0.8797 (pmm) REVERT: TB 194 ASP cc_start: 0.8499 (m-30) cc_final: 0.7861 (m-30) REVERT: TB 222 GLU cc_start: 0.9119 (tt0) cc_final: 0.8370 (tm-30) REVERT: TB 251 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8853 (mt-10) REVERT: TB 254 ASP cc_start: 0.9408 (m-30) cc_final: 0.9161 (m-30) REVERT: TB 272 ASP cc_start: 0.8622 (p0) cc_final: 0.7947 (p0) REVERT: TB 328 TRP cc_start: 0.9198 (m100) cc_final: 0.8683 (m100) REVERT: TB 362 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8485 (mm-30) REVERT: TB 367 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9044 (t0) REVERT: TB 389 MET cc_start: 0.9275 (mtm) cc_final: 0.9020 (ttm) REVERT: LA 120 VAL cc_start: 0.9233 (t) cc_final: 0.8993 (m) REVERT: LA 192 MET cc_start: 0.9310 (tpt) cc_final: 0.7845 (tpp) REVERT: LA 202 GLU cc_start: 0.8963 (tt0) cc_final: 0.8623 (tp30) REVERT: LA 253 LYS cc_start: 0.9125 (tttp) cc_final: 0.8877 (ttpp) REVERT: LA 337 ASP cc_start: 0.8888 (m-30) cc_final: 0.8503 (m-30) REVERT: LA 361 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8147 (tp30) REVERT: LA 363 LYS cc_start: 0.8949 (mttt) cc_final: 0.8415 (mtpp) REVERT: LB 119 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8843 (pm20) REVERT: LB 126 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8249 (pm20) REVERT: LB 192 MET cc_start: 0.9415 (tpt) cc_final: 0.7384 (mtt) REVERT: LB 202 GLU cc_start: 0.8985 (tp30) cc_final: 0.8709 (tp30) REVERT: LF 117 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8895 (mm) REVERT: LF 153 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8434 (mt-10) REVERT: LF 192 MET cc_start: 0.6843 (ttp) cc_final: 0.5824 (mmt) REVERT: LF 195 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8926 (mm-40) REVERT: LF 202 GLU cc_start: 0.9048 (tt0) cc_final: 0.8361 (tp30) REVERT: LF 206 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8637 (mm110) REVERT: LF 306 MET cc_start: 0.9216 (ttm) cc_final: 0.8908 (ttm) REVERT: LF 337 ASP cc_start: 0.9085 (m-30) cc_final: 0.8454 (m-30) REVERT: LF 361 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: LF 365 TYR cc_start: 0.9283 (p90) cc_final: 0.8839 (p90) REVERT: LE 105 ASP cc_start: 0.8741 (t70) cc_final: 0.8533 (t0) REVERT: LE 122 MET cc_start: 0.9556 (mmt) cc_final: 0.9173 (mmm) REVERT: LE 133 GLU cc_start: 0.8434 (mp0) cc_final: 0.8224 (mp0) REVERT: LE 192 MET cc_start: 0.8832 (tpt) cc_final: 0.7039 (mtt) REVERT: LE 361 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: LD 105 ASP cc_start: 0.8267 (m-30) cc_final: 0.7569 (t0) REVERT: LD 120 VAL cc_start: 0.9357 (t) cc_final: 0.9146 (p) REVERT: LD 192 MET cc_start: 0.7816 (ttt) cc_final: 0.6693 (mtt) REVERT: LD 253 LYS cc_start: 0.9360 (ttpt) cc_final: 0.9140 (ttmm) REVERT: LD 281 ASN cc_start: 0.8294 (t0) cc_final: 0.8079 (t0) REVERT: LD 287 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8656 (mm-30) REVERT: LC 171 THR cc_start: 0.9050 (m) cc_final: 0.8677 (p) REVERT: LC 192 MET cc_start: 0.9244 (tpt) cc_final: 0.7414 (mtt) REVERT: LC 197 MET cc_start: 0.8923 (mmm) cc_final: 0.8146 (mpt) REVERT: LC 290 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8529 (mtm-85) REVERT: LC 337 ASP cc_start: 0.8932 (m-30) cc_final: 0.8506 (m-30) REVERT: LC 366 GLU cc_start: 0.8994 (mp0) cc_final: 0.8777 (mm-30) outliers start: 60 outliers final: 21 residues processed: 634 average time/residue: 1.6714 time to fit residues: 1273.4059 Evaluate side-chains 575 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 547 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TG residue 64 GLU Chi-restraints excluded: chain TA residue 27 ASP Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 175 VAL Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TA residue 254 ASP Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 135 VAL 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 117 LEU 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 361 GLU Chi-restraints excluded: chain LD residue 333 SER Chi-restraints excluded: chain LC residue 290 ARG Chi-restraints excluded: chain LC residue 359 ASP 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 109 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 165 optimal weight: 50.0000 chunk 356 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 342 optimal weight: 0.0970 chunk 329 optimal weight: 8.9990 overall best weight: 4.0184 ------------------------------------------------------------------------------- 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 9 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 31 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 9 GLN TI 31 GLN TI 83 GLN TA 260 HIS ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN LA 380 HIS LB 349 HIS LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 380 HIS LE 376 ASN ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 356 ASN LC 136 ASN LC 239 GLN LC 270 GLN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 376 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.067005 restraints weight = 51288.739| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.41 r_work: 0.2669 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28662 Z= 0.188 Angle : 0.557 9.252 38989 Z= 0.297 Chirality : 0.046 0.330 4385 Planarity : 0.003 0.045 5287 Dihedral : 5.663 66.286 4027 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.10 % Allowed : 19.62 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 3635 helix: 1.75 (0.19), residues: 727 sheet: 0.28 (0.16), residues: 1016 loop : -0.64 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPTB 65 HIS 0.006 0.001 HISLE 349 PHE 0.015 0.001 PHETA 354 TYR 0.026 0.002 TYRTC 290 ARG 0.010 0.000 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 820) hydrogen bonds : angle 5.27727 ( 2304) metal coordination : bond 0.00141 ( 6) covalent geometry : bond 0.00422 (28656) covalent geometry : angle 0.55678 (38989) *********************** 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 612 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 548 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8585 (t0) cc_final: 0.8200 (t70) REVERT: TC 22 SER cc_start: 0.9124 (t) cc_final: 0.8590 (m) REVERT: TC 65 TRP cc_start: 0.8168 (m-90) cc_final: 0.7838 (m-90) REVERT: TC 80 TYR cc_start: 0.9323 (t80) cc_final: 0.9018 (t80) REVERT: TC 120 ASP cc_start: 0.8925 (t0) cc_final: 0.8646 (t0) REVERT: TC 131 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7777 (mptt) REVERT: TC 155 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8607 (tp30) REVERT: TC 174 ASN cc_start: 0.8817 (t0) cc_final: 0.8580 (p0) REVERT: TC 179 THR cc_start: 0.8657 (p) cc_final: 0.7964 (t) REVERT: TC 194 ASP cc_start: 0.7737 (t0) cc_final: 0.7108 (t70) REVERT: TC 251 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9257 (mt-10) REVERT: TC 260 HIS cc_start: 0.9171 (p-80) cc_final: 0.8782 (p-80) REVERT: TC 294 ASP cc_start: 0.8891 (m-30) cc_final: 0.8619 (m-30) REVERT: TC 352 CYS cc_start: 0.8664 (t) cc_final: 0.8241 (t) REVERT: TC 363 GLN cc_start: 0.9169 (tp40) cc_final: 0.8396 (tp40) REVERT: TC 367 ASP cc_start: 0.9122 (m-30) cc_final: 0.8213 (m-30) REVERT: TC 372 ASN cc_start: 0.9023 (m-40) cc_final: 0.8304 (p0) REVERT: TC 400 ASP cc_start: 0.8769 (t70) cc_final: 0.8416 (p0) REVERT: TC 407 MET cc_start: 0.9349 (mpp) cc_final: 0.8982 (mpp) REVERT: TC 411 ASN cc_start: 0.9239 (m-40) cc_final: 0.8641 (m-40) REVERT: TD 39 GLU cc_start: 0.8937 (tt0) cc_final: 0.8603 (tt0) REVERT: TD 58 ASP cc_start: 0.8996 (t70) cc_final: 0.8486 (t0) REVERT: TD 83 GLN cc_start: 0.9081 (mt0) cc_final: 0.8646 (tt0) REVERT: TD 85 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8544 (mt-10) REVERT: TE 58 ASP cc_start: 0.8902 (t70) cc_final: 0.8418 (t70) REVERT: TE 83 GLN cc_start: 0.9051 (tt0) cc_final: 0.8787 (tt0) REVERT: TE 85 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8784 (mt-10) REVERT: TF 58 ASP cc_start: 0.8888 (t70) cc_final: 0.8615 (t70) REVERT: TF 83 GLN cc_start: 0.8919 (mt0) cc_final: 0.8425 (tt0) REVERT: TG 58 ASP cc_start: 0.9068 (t70) cc_final: 0.8764 (t0) REVERT: TG 64 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: TG 71 ASP cc_start: 0.9126 (t0) cc_final: 0.8822 (t0) REVERT: TG 83 GLN cc_start: 0.9091 (mt0) cc_final: 0.8799 (tt0) REVERT: TH 7 ASN cc_start: 0.8697 (m110) cc_final: 0.8461 (m110) REVERT: TH 29 ASP cc_start: 0.9410 (t0) cc_final: 0.9209 (t70) REVERT: TH 52 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8622 (mt-10) REVERT: TH 58 ASP cc_start: 0.8989 (t70) cc_final: 0.8642 (t70) REVERT: TH 83 GLN cc_start: 0.8975 (mt0) cc_final: 0.8592 (mt0) REVERT: TH 85 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8903 (mt-10) REVERT: TH 92 THR cc_start: 0.9644 (m) cc_final: 0.9366 (p) REVERT: TA 97 ILE cc_start: 0.9608 (pt) cc_final: 0.9373 (pp) REVERT: TA 112 PHE cc_start: 0.8801 (m-80) cc_final: 0.8453 (m-80) REVERT: TA 131 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8527 (mppt) REVERT: TA 194 ASP cc_start: 0.8314 (t70) cc_final: 0.7341 (t0) REVERT: TA 222 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: TA 251 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9020 (mt-10) REVERT: TA 280 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8669 (mt-10) REVERT: TA 360 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8901 (tp30) REVERT: TA 389 MET cc_start: 0.9158 (mtt) cc_final: 0.8800 (mtm) REVERT: TB 22 SER cc_start: 0.9315 (t) cc_final: 0.8847 (p) REVERT: TB 133 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6831 (mtm180) REVERT: TB 138 ASN cc_start: 0.9017 (t0) cc_final: 0.8806 (t0) REVERT: TB 171 ASP cc_start: 0.9439 (t0) cc_final: 0.8692 (p0) REVERT: TB 178 MET cc_start: 0.9217 (ptm) cc_final: 0.8858 (pmm) REVERT: TB 194 ASP cc_start: 0.8578 (m-30) cc_final: 0.7865 (m-30) REVERT: TB 251 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8858 (mt-10) REVERT: TB 254 ASP cc_start: 0.9412 (m-30) cc_final: 0.9166 (m-30) REVERT: TB 272 ASP cc_start: 0.8562 (p0) cc_final: 0.7927 (p0) REVERT: TB 328 TRP cc_start: 0.9252 (m100) cc_final: 0.8652 (m100) REVERT: TB 362 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8445 (mm-30) REVERT: TB 367 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9069 (t0) REVERT: LA 192 MET cc_start: 0.9347 (tpt) cc_final: 0.7878 (tpp) REVERT: LA 281 ASN cc_start: 0.7901 (t0) cc_final: 0.7698 (t0) REVERT: LA 337 ASP cc_start: 0.9002 (m-30) cc_final: 0.8605 (m-30) REVERT: LA 361 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8156 (tp30) REVERT: LA 363 LYS cc_start: 0.8947 (mttt) cc_final: 0.8415 (mtpp) REVERT: LB 119 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8824 (pm20) REVERT: LB 126 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8253 (pm20) REVERT: LB 192 MET cc_start: 0.9435 (tpt) cc_final: 0.7393 (mtt) REVERT: LB 202 GLU cc_start: 0.8990 (tp30) cc_final: 0.8693 (tp30) REVERT: LF 153 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8448 (mt-10) REVERT: LF 192 MET cc_start: 0.6889 (ttp) cc_final: 0.5842 (mpt) REVERT: LF 202 GLU cc_start: 0.9042 (tt0) cc_final: 0.8381 (tp30) REVERT: LF 206 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8693 (mm-40) REVERT: LF 337 ASP cc_start: 0.9181 (m-30) cc_final: 0.8551 (m-30) REVERT: LF 358 GLN cc_start: 0.8749 (tp40) cc_final: 0.8545 (mp10) REVERT: LF 361 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: LF 363 LYS cc_start: 0.9332 (mtmt) cc_final: 0.8875 (mtpt) REVERT: LF 365 TYR cc_start: 0.9323 (p90) cc_final: 0.8847 (p90) REVERT: LE 105 ASP cc_start: 0.8812 (t70) cc_final: 0.8563 (t0) REVERT: LE 133 GLU cc_start: 0.8485 (mp0) cc_final: 0.8264 (mp0) REVERT: LE 192 MET cc_start: 0.8829 (tpt) cc_final: 0.7072 (mtt) REVERT: LE 361 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: LD 105 ASP cc_start: 0.8358 (m-30) cc_final: 0.7668 (t0) REVERT: LD 120 VAL cc_start: 0.9363 (t) cc_final: 0.9152 (p) REVERT: LD 192 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6756 (mtt) REVERT: LD 197 MET cc_start: 0.4548 (mpt) cc_final: 0.4318 (mpt) REVERT: LD 253 LYS cc_start: 0.9374 (ttpt) cc_final: 0.9148 (ttmt) REVERT: LD 287 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8624 (mm-30) REVERT: LD 361 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8746 (tt0) REVERT: LC 171 THR cc_start: 0.9108 (m) cc_final: 0.8724 (p) REVERT: LC 192 MET cc_start: 0.9268 (tpt) cc_final: 0.7426 (mtt) REVERT: LC 197 MET cc_start: 0.9000 (mmm) cc_final: 0.8274 (mpt) REVERT: LC 290 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8476 (mtm-85) REVERT: LC 366 GLU cc_start: 0.9020 (mp0) cc_final: 0.8780 (mm-30) outliers start: 64 outliers final: 27 residues processed: 590 average time/residue: 1.3638 time to fit residues: 945.7640 Evaluate side-chains 561 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 525 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 7 ASN Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TG residue 64 GLU 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 175 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TA residue 254 ASP Chi-restraints excluded: chain TB residue 48 LEU Chi-restraints excluded: chain TB residue 133 ARG Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 182 THR Chi-restraints excluded: chain TB residue 247 LEU 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 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 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 359 ASP 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 151 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 chunk 163 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 31 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 31 GLN TI 83 GLN TA 260 HIS ** LA 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 376 ASN ** LB 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 161 GLN LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 136 ASN LE 356 ASN LE 376 ASN LD 356 ASN LC 270 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.092319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065050 restraints weight = 51544.337| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.38 r_work: 0.2631 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28662 Z= 0.280 Angle : 0.610 14.784 38989 Z= 0.325 Chirality : 0.047 0.348 4385 Planarity : 0.004 0.054 5287 Dihedral : 5.749 62.927 4027 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.40 % Allowed : 19.85 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3635 helix: 1.62 (0.19), residues: 727 sheet: 0.13 (0.16), residues: 1047 loop : -0.61 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPTB 65 HIS 0.008 0.001 HISLE 349 PHE 0.023 0.002 PHETA 163 TYR 0.027 0.002 TYRTB 410 ARG 0.010 0.001 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 820) hydrogen bonds : angle 5.41859 ( 2304) metal coordination : bond 0.00229 ( 6) covalent geometry : bond 0.00623 (28656) covalent geometry : angle 0.60974 (38989) *********************** 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 584 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 511 time to evaluate : 3.095 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: 0.8393 (t70) REVERT: TC 22 SER cc_start: 0.9126 (t) cc_final: 0.8600 (m) REVERT: TC 65 TRP cc_start: 0.8185 (m-90) cc_final: 0.7859 (m-90) REVERT: TC 120 ASP cc_start: 0.8955 (t0) cc_final: 0.8656 (t0) REVERT: TC 131 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7767 (mptt) REVERT: TC 155 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8606 (tp30) REVERT: TC 174 ASN cc_start: 0.8808 (t0) cc_final: 0.8562 (p0) REVERT: TC 179 THR cc_start: 0.8596 (p) cc_final: 0.7850 (t) REVERT: TC 251 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9149 (mt-10) REVERT: TC 260 HIS cc_start: 0.9236 (p-80) cc_final: 0.8946 (p-80) REVERT: TC 294 ASP cc_start: 0.8913 (m-30) cc_final: 0.8654 (m-30) REVERT: TC 352 CYS cc_start: 0.8728 (t) cc_final: 0.8305 (t) REVERT: TC 363 GLN cc_start: 0.9172 (tp40) cc_final: 0.8389 (tp40) REVERT: TC 367 ASP cc_start: 0.9160 (m-30) cc_final: 0.8197 (m-30) REVERT: TC 372 ASN cc_start: 0.9021 (m-40) cc_final: 0.8311 (p0) REVERT: TC 400 ASP cc_start: 0.8819 (t70) cc_final: 0.8304 (p0) REVERT: TC 407 MET cc_start: 0.9364 (mpp) cc_final: 0.9006 (mpp) REVERT: TC 411 ASN cc_start: 0.9259 (m-40) cc_final: 0.8660 (m-40) REVERT: TD 39 GLU cc_start: 0.8967 (tt0) cc_final: 0.8652 (tt0) REVERT: TD 58 ASP cc_start: 0.8998 (t70) cc_final: 0.8474 (t0) REVERT: TD 83 GLN cc_start: 0.9094 (mt0) cc_final: 0.8609 (tt0) REVERT: TD 85 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8562 (mt-10) REVERT: TE 58 ASP cc_start: 0.8907 (t70) cc_final: 0.8397 (t70) REVERT: TF 58 ASP cc_start: 0.8864 (t70) cc_final: 0.8605 (t70) REVERT: TF 83 GLN cc_start: 0.9021 (mt0) cc_final: 0.8401 (tt0) REVERT: TG 7 ASN cc_start: 0.8872 (m-40) cc_final: 0.8543 (t0) REVERT: TG 24 GLU cc_start: 0.9243 (mm-30) cc_final: 0.9036 (mm-30) REVERT: TG 58 ASP cc_start: 0.9052 (t70) cc_final: 0.8778 (t0) REVERT: TG 71 ASP cc_start: 0.9126 (t0) cc_final: 0.8662 (t0) REVERT: TG 83 GLN cc_start: 0.9146 (mt0) cc_final: 0.8795 (tt0) REVERT: TH 29 ASP cc_start: 0.9414 (t0) cc_final: 0.9202 (t0) REVERT: TH 52 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8692 (mt-10) REVERT: TH 58 ASP cc_start: 0.8980 (t70) cc_final: 0.8606 (t70) REVERT: TH 83 GLN cc_start: 0.8971 (mt0) cc_final: 0.8565 (mt0) REVERT: TH 85 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8928 (mt-10) REVERT: TH 92 THR cc_start: 0.9633 (m) cc_final: 0.9361 (p) REVERT: TI 11 SER cc_start: 0.9106 (m) cc_final: 0.8779 (t) REVERT: TA 97 ILE cc_start: 0.9604 (pt) cc_final: 0.9370 (pp) REVERT: TA 131 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8504 (mppt) REVERT: TA 155 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (tp30) REVERT: TA 194 ASP cc_start: 0.8350 (t70) cc_final: 0.7423 (t0) REVERT: TA 222 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: TA 251 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8991 (mt-10) REVERT: TA 280 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8756 (mt-10) REVERT: TA 360 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8918 (tp30) REVERT: TA 389 MET cc_start: 0.9139 (mtt) cc_final: 0.8753 (mtm) REVERT: TB 22 SER cc_start: 0.9308 (t) cc_final: 0.8824 (p) REVERT: TB 65 TRP cc_start: 0.8279 (m-90) cc_final: 0.7908 (m-90) REVERT: TB 133 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6794 (mtm180) REVERT: TB 171 ASP cc_start: 0.9445 (t0) cc_final: 0.9163 (t0) REVERT: TB 178 MET cc_start: 0.9213 (ptm) cc_final: 0.8820 (pmm) REVERT: TB 194 ASP cc_start: 0.8564 (m-30) cc_final: 0.7831 (m-30) REVERT: TB 251 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8769 (mt-10) REVERT: TB 272 ASP cc_start: 0.8534 (p0) cc_final: 0.7900 (p0) REVERT: TB 328 TRP cc_start: 0.9256 (m100) cc_final: 0.8708 (m100) REVERT: TB 362 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8474 (mm-30) REVERT: TB 367 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9059 (t0) REVERT: LA 192 MET cc_start: 0.9354 (tpt) cc_final: 0.7920 (tpp) REVERT: LA 281 ASN cc_start: 0.8084 (t0) cc_final: 0.7876 (t0) REVERT: LA 337 ASP cc_start: 0.9027 (m-30) cc_final: 0.8724 (m-30) REVERT: LA 361 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8173 (tp30) REVERT: LA 363 LYS cc_start: 0.9001 (mttt) cc_final: 0.8475 (mtpp) REVERT: LB 119 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8810 (pm20) REVERT: LB 126 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8293 (pm20) REVERT: LB 164 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7454 (mm-30) REVERT: LB 192 MET cc_start: 0.9428 (tpt) cc_final: 0.7378 (mtt) REVERT: LB 202 GLU cc_start: 0.9024 (tp30) cc_final: 0.8481 (tp30) REVERT: LF 192 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.5679 (mpt) REVERT: LF 202 GLU cc_start: 0.9057 (tt0) cc_final: 0.8348 (tp30) REVERT: LF 206 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8723 (mm-40) REVERT: LF 337 ASP cc_start: 0.9213 (m-30) cc_final: 0.8572 (m-30) REVERT: LF 358 GLN cc_start: 0.8755 (tp40) cc_final: 0.8499 (mp10) REVERT: LF 361 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: LF 363 LYS cc_start: 0.9350 (mtmt) cc_final: 0.8847 (mtpt) REVERT: LF 365 TYR cc_start: 0.9323 (p90) cc_final: 0.8772 (p90) REVERT: LE 105 ASP cc_start: 0.8848 (t70) cc_final: 0.8614 (t0) REVERT: LE 133 GLU cc_start: 0.8420 (mp0) cc_final: 0.8203 (mp0) REVERT: LE 192 MET cc_start: 0.8801 (tpt) cc_final: 0.7114 (mtt) REVERT: LE 361 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: LD 105 ASP cc_start: 0.8439 (m-30) cc_final: 0.7727 (t0) REVERT: LD 120 VAL cc_start: 0.9313 (t) cc_final: 0.9108 (p) REVERT: LD 192 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6732 (mtt) REVERT: LD 197 MET cc_start: 0.4692 (mpt) cc_final: 0.4179 (mpt) REVERT: LD 253 LYS cc_start: 0.9351 (ttpt) cc_final: 0.9104 (ttmt) REVERT: LD 287 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8552 (mm-30) REVERT: LD 361 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: LC 122 MET cc_start: 0.9495 (mmm) cc_final: 0.9257 (mmp) REVERT: LC 171 THR cc_start: 0.9156 (m) cc_final: 0.8832 (p) REVERT: LC 192 MET cc_start: 0.9268 (tpt) cc_final: 0.7432 (mtt) REVERT: LC 197 MET cc_start: 0.9008 (mmm) cc_final: 0.8294 (mpt) REVERT: LC 290 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8452 (mtm-85) REVERT: LC 358 GLN cc_start: 0.8878 (tt0) cc_final: 0.8244 (pm20) REVERT: LC 366 GLU cc_start: 0.9041 (mp0) cc_final: 0.8785 (mm-30) outliers start: 73 outliers final: 41 residues processed: 559 average time/residue: 1.4049 time to fit residues: 923.7633 Evaluate side-chains 551 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 500 time to evaluate : 3.258 ------------------------------------------------------------------------------- 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 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 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 222 GLU Chi-restraints excluded: chain TA residue 254 ASP 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 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 244 SER Chi-restraints excluded: chain TB residue 247 LEU Chi-restraints excluded: chain TB residue 367 ASP Chi-restraints excluded: chain LA residue 147 VAL Chi-restraints excluded: chain LA residue 168 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 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 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 301 ILE 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 306 MET Chi-restraints excluded: chain LC residue 359 ASP Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 170 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 326 optimal weight: 6.9990 chunk 218 optimal weight: 0.4980 chunk 231 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- 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 ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 31 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 LD 239 GLN LD 356 ASN LC 239 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.065814 restraints weight = 51424.910| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.40 r_work: 0.2644 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28662 Z= 0.213 Angle : 0.589 9.392 38989 Z= 0.314 Chirality : 0.046 0.313 4385 Planarity : 0.003 0.046 5287 Dihedral : 5.742 64.880 4027 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.23 % Allowed : 19.85 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3635 helix: 1.58 (0.19), residues: 727 sheet: 0.14 (0.16), residues: 1014 loop : -0.65 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPTB 65 HIS 0.005 0.001 HISLE 349 PHE 0.016 0.001 PHETA 163 TYR 0.026 0.002 TYRTB 410 ARG 0.010 0.000 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 820) hydrogen bonds : angle 5.39611 ( 2304) metal coordination : bond 0.00149 ( 6) covalent geometry : bond 0.00477 (28656) covalent geometry : angle 0.58868 (38989) *********************** 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 595 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 527 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8670 (t0) cc_final: 0.8406 (t70) REVERT: TC 22 SER cc_start: 0.9113 (t) cc_final: 0.8586 (m) REVERT: TC 65 TRP cc_start: 0.8122 (m-90) cc_final: 0.7813 (m-90) REVERT: TC 80 TYR cc_start: 0.9318 (t80) cc_final: 0.8876 (t80) REVERT: TC 117 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7244 (ttpp) REVERT: TC 120 ASP cc_start: 0.8949 (t0) cc_final: 0.8636 (t0) REVERT: TC 131 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7817 (mptt) REVERT: TC 155 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8551 (tp30) REVERT: TC 174 ASN cc_start: 0.8815 (t0) cc_final: 0.8583 (p0) REVERT: TC 179 THR cc_start: 0.8604 (p) cc_final: 0.7905 (t) REVERT: TC 251 GLU cc_start: 0.9511 (mt-10) cc_final: 0.9159 (mt-10) REVERT: TC 260 HIS cc_start: 0.9207 (p-80) cc_final: 0.8967 (p-80) REVERT: TC 294 ASP cc_start: 0.8917 (m-30) cc_final: 0.8666 (m-30) REVERT: TC 352 CYS cc_start: 0.8713 (t) cc_final: 0.8266 (t) REVERT: TC 363 GLN cc_start: 0.9161 (tp40) cc_final: 0.8378 (tp40) REVERT: TC 367 ASP cc_start: 0.9151 (m-30) cc_final: 0.8167 (m-30) REVERT: TC 372 ASN cc_start: 0.9003 (m-40) cc_final: 0.8296 (p0) REVERT: TC 400 ASP cc_start: 0.8724 (t70) cc_final: 0.8200 (p0) REVERT: TC 407 MET cc_start: 0.9359 (mpp) cc_final: 0.8999 (mpp) REVERT: TC 411 ASN cc_start: 0.9243 (m-40) cc_final: 0.8641 (m-40) REVERT: TD 39 GLU cc_start: 0.8943 (tt0) cc_final: 0.8570 (tt0) REVERT: TD 58 ASP cc_start: 0.9027 (t70) cc_final: 0.8552 (t0) REVERT: TD 83 GLN cc_start: 0.9088 (mt0) cc_final: 0.8577 (tt0) REVERT: TD 85 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8585 (mt-10) REVERT: TE 58 ASP cc_start: 0.8932 (t70) cc_final: 0.8458 (t70) REVERT: TE 85 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8688 (mt-10) REVERT: TF 39 GLU cc_start: 0.9041 (tt0) cc_final: 0.8665 (tt0) REVERT: TF 58 ASP cc_start: 0.8915 (t70) cc_final: 0.8659 (t70) REVERT: TF 83 GLN cc_start: 0.8978 (mt0) cc_final: 0.8437 (tt0) REVERT: TG 7 ASN cc_start: 0.8845 (m-40) cc_final: 0.8567 (t0) REVERT: TG 58 ASP cc_start: 0.9064 (t70) cc_final: 0.8823 (t0) REVERT: TG 71 ASP cc_start: 0.9131 (t0) cc_final: 0.8795 (t0) REVERT: TG 83 GLN cc_start: 0.9127 (mt0) cc_final: 0.8804 (tt0) REVERT: TG 105 ASP cc_start: 0.9102 (m-30) cc_final: 0.8869 (m-30) REVERT: TH 29 ASP cc_start: 0.9380 (t0) cc_final: 0.9178 (t70) REVERT: TH 52 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8677 (mt-10) REVERT: TH 58 ASP cc_start: 0.9017 (t70) cc_final: 0.8651 (t70) REVERT: TH 83 GLN cc_start: 0.8971 (mt0) cc_final: 0.8575 (mt0) REVERT: TH 85 GLU cc_start: 0.9356 (mt-10) cc_final: 0.8880 (mt-10) REVERT: TH 92 THR cc_start: 0.9634 (m) cc_final: 0.9360 (p) REVERT: TA 97 ILE cc_start: 0.9600 (pt) cc_final: 0.9356 (pp) REVERT: TA 131 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8548 (mppt) REVERT: TA 155 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8709 (tp30) REVERT: TA 171 ASP cc_start: 0.9117 (t0) cc_final: 0.8651 (t0) REVERT: TA 194 ASP cc_start: 0.8342 (t70) cc_final: 0.7389 (t0) REVERT: TA 222 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8300 (tp30) REVERT: TA 251 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8985 (mt-10) REVERT: TA 280 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8771 (mt-10) REVERT: TA 360 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8922 (tp30) REVERT: TA 367 ASP cc_start: 0.9073 (m-30) cc_final: 0.8798 (m-30) REVERT: TA 389 MET cc_start: 0.9145 (mtt) cc_final: 0.8746 (mtm) REVERT: TB 22 SER cc_start: 0.9314 (t) cc_final: 0.8835 (p) REVERT: TB 65 TRP cc_start: 0.8270 (m-90) cc_final: 0.7807 (m-90) REVERT: TB 133 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6792 (mtm180) REVERT: TB 171 ASP cc_start: 0.9444 (t0) cc_final: 0.8702 (p0) REVERT: TB 194 ASP cc_start: 0.8531 (m-30) cc_final: 0.7853 (m-30) REVERT: TB 222 GLU cc_start: 0.9097 (tt0) cc_final: 0.8372 (tm-30) REVERT: TB 246 LYS cc_start: 0.9084 (mttp) cc_final: 0.8830 (mmmt) REVERT: TB 251 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8835 (mt-10) REVERT: TB 254 ASP cc_start: 0.9438 (m-30) cc_final: 0.9197 (m-30) REVERT: TB 272 ASP cc_start: 0.8548 (p0) cc_final: 0.7916 (p0) REVERT: TB 328 TRP cc_start: 0.9242 (m100) cc_final: 0.8733 (m100) REVERT: TB 362 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8457 (mm-30) REVERT: LA 192 MET cc_start: 0.9364 (tpt) cc_final: 0.7916 (tpp) REVERT: LA 281 ASN cc_start: 0.8017 (t0) cc_final: 0.7807 (t0) REVERT: LA 337 ASP cc_start: 0.9014 (m-30) cc_final: 0.8690 (m-30) REVERT: LA 361 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8124 (tp30) REVERT: LA 363 LYS cc_start: 0.8961 (mttt) cc_final: 0.8453 (mtpp) REVERT: LB 119 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8801 (pm20) REVERT: LB 126 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8315 (pm20) REVERT: LB 192 MET cc_start: 0.9444 (tpt) cc_final: 0.7409 (mtt) REVERT: LB 202 GLU cc_start: 0.9011 (tp30) cc_final: 0.8699 (tp30) REVERT: LF 153 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8511 (mt-10) REVERT: LF 192 MET cc_start: 0.6664 (ttp) cc_final: 0.5525 (mpt) REVERT: LF 202 GLU cc_start: 0.9066 (tt0) cc_final: 0.8366 (tp30) REVERT: LF 206 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8745 (mm-40) REVERT: LF 337 ASP cc_start: 0.9165 (m-30) cc_final: 0.8544 (m-30) REVERT: LF 358 GLN cc_start: 0.8764 (tp40) cc_final: 0.8492 (mp10) REVERT: LF 361 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: LF 363 LYS cc_start: 0.9320 (mtmt) cc_final: 0.9054 (mtpt) REVERT: LF 365 TYR cc_start: 0.9343 (p90) cc_final: 0.8830 (p90) REVERT: LE 105 ASP cc_start: 0.8817 (t70) cc_final: 0.8587 (t0) REVERT: LE 122 MET cc_start: 0.9529 (mmt) cc_final: 0.9120 (mmm) REVERT: LE 133 GLU cc_start: 0.8432 (mp0) cc_final: 0.8146 (mp0) REVERT: LE 192 MET cc_start: 0.8845 (tpt) cc_final: 0.7095 (mtt) REVERT: LE 361 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (tt0) REVERT: LD 105 ASP cc_start: 0.8398 (m-30) cc_final: 0.7699 (t0) REVERT: LD 192 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6767 (mtt) REVERT: LD 253 LYS cc_start: 0.9360 (ttpt) cc_final: 0.9113 (ttmm) REVERT: LD 287 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8563 (mm-30) REVERT: LD 361 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: LD 367 ASP cc_start: 0.9011 (t0) cc_final: 0.8765 (t0) REVERT: LC 122 MET cc_start: 0.9513 (mmm) cc_final: 0.9274 (mmp) REVERT: LC 171 THR cc_start: 0.9166 (m) cc_final: 0.8824 (p) REVERT: LC 192 MET cc_start: 0.9279 (tpt) cc_final: 0.7433 (mtt) REVERT: LC 197 MET cc_start: 0.9007 (mmm) cc_final: 0.8302 (mpt) REVERT: LC 290 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8457 (mtm-85) REVERT: LC 358 GLN cc_start: 0.8847 (tt0) cc_final: 0.8424 (pm20) REVERT: LC 366 GLU cc_start: 0.9036 (mp0) cc_final: 0.8806 (mm-30) outliers start: 68 outliers final: 35 residues processed: 571 average time/residue: 1.3938 time to fit residues: 937.3266 Evaluate side-chains 553 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 510 time to evaluate : 3.143 ------------------------------------------------------------------------------- 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 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 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 TA residue 254 ASP 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 168 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 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 105 ASP 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 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 290 ARG Chi-restraints excluded: chain LC residue 306 MET Chi-restraints excluded: chain LC residue 375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 181 optimal weight: 40.0000 chunk 285 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 189 optimal weight: 0.0010 chunk 155 optimal weight: 20.0000 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** LA 376 ASN LB 356 ASN ** LF 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 376 ASN ** LD 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 356 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068181 restraints weight = 50970.792| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.41 r_work: 0.2693 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28662 Z= 0.133 Angle : 0.568 12.284 38989 Z= 0.300 Chirality : 0.045 0.210 4385 Planarity : 0.003 0.045 5287 Dihedral : 5.698 68.179 4027 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 1.41 % Allowed : 20.97 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 3635 helix: 1.63 (0.19), residues: 733 sheet: 0.21 (0.16), residues: 1008 loop : -0.67 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPTB 65 HIS 0.004 0.001 HISLE 349 PHE 0.015 0.001 PHETA 354 TYR 0.026 0.001 TYRTC 290 ARG 0.010 0.000 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 820) hydrogen bonds : angle 5.31623 ( 2304) metal coordination : bond 0.00080 ( 6) covalent geometry : bond 0.00299 (28656) covalent geometry : angle 0.56779 (38989) ********************** 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 586 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 543 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: TC 7 ASP cc_start: 0.8640 (t0) cc_final: 0.8196 (t70) REVERT: TC 22 SER cc_start: 0.9099 (t) cc_final: 0.8554 (m) REVERT: TC 59 PHE cc_start: 0.8583 (m-80) cc_final: 0.8226 (m-80) REVERT: TC 80 TYR cc_start: 0.9279 (t80) cc_final: 0.8982 (t80) REVERT: TC 114 MET cc_start: 0.8086 (tpt) cc_final: 0.7707 (tpt) REVERT: TC 117 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7196 (ttpp) REVERT: TC 120 ASP cc_start: 0.8930 (t0) cc_final: 0.8606 (t0) REVERT: TC 131 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7729 (mptt) REVERT: TC 155 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8493 (tp30) REVERT: TC 171 ASP cc_start: 0.9287 (t0) cc_final: 0.9079 (t0) REVERT: TC 194 ASP cc_start: 0.8390 (m-30) cc_final: 0.7614 (m-30) REVERT: TC 238 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8762 (ptmm) REVERT: TC 251 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9145 (mt-10) REVERT: TC 260 HIS cc_start: 0.9107 (p-80) cc_final: 0.8757 (p-80) REVERT: TC 294 ASP cc_start: 0.8897 (m-30) cc_final: 0.8613 (m-30) REVERT: TC 352 CYS cc_start: 0.8680 (t) cc_final: 0.8223 (t) REVERT: TC 362 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8668 (mp0) REVERT: TC 363 GLN cc_start: 0.9164 (tp40) cc_final: 0.8367 (tp40) REVERT: TC 367 ASP cc_start: 0.9164 (m-30) cc_final: 0.7969 (m-30) REVERT: TC 372 ASN cc_start: 0.8975 (m-40) cc_final: 0.8313 (p0) REVERT: TC 400 ASP cc_start: 0.8711 (t70) cc_final: 0.8178 (p0) REVERT: TC 407 MET cc_start: 0.9363 (mpp) cc_final: 0.9068 (mpp) REVERT: TC 411 ASN cc_start: 0.9230 (m-40) cc_final: 0.8670 (m-40) REVERT: TD 39 GLU cc_start: 0.8887 (tt0) cc_final: 0.8595 (tt0) REVERT: TD 58 ASP cc_start: 0.9027 (t70) cc_final: 0.8591 (t70) REVERT: TD 83 GLN cc_start: 0.9047 (mt0) cc_final: 0.8623 (tt0) REVERT: TD 85 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8500 (mt-10) REVERT: TE 58 ASP cc_start: 0.8868 (t70) cc_final: 0.8399 (t70) REVERT: TE 85 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8720 (mt-10) REVERT: TF 39 GLU cc_start: 0.8993 (tt0) cc_final: 0.8512 (tt0) REVERT: TF 58 ASP cc_start: 0.8929 (t70) cc_final: 0.8723 (t70) REVERT: TF 83 GLN cc_start: 0.8846 (mt0) cc_final: 0.8346 (tt0) REVERT: TG 7 ASN cc_start: 0.8792 (m-40) cc_final: 0.8537 (t0) REVERT: TG 58 ASP cc_start: 0.9022 (t70) cc_final: 0.8693 (t0) REVERT: TG 71 ASP cc_start: 0.9111 (t0) cc_final: 0.8848 (t0) REVERT: TG 83 GLN cc_start: 0.9044 (mt0) cc_final: 0.8747 (tt0) REVERT: TG 105 ASP cc_start: 0.9063 (m-30) cc_final: 0.8826 (m-30) REVERT: TH 29 ASP cc_start: 0.9397 (t0) cc_final: 0.9191 (t70) REVERT: TH 52 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8658 (mt-10) REVERT: TH 58 ASP cc_start: 0.9056 (t70) cc_final: 0.8694 (t70) REVERT: TH 83 GLN cc_start: 0.8953 (mt0) cc_final: 0.8440 (tt0) REVERT: TH 85 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8665 (mt-10) REVERT: TH 92 THR cc_start: 0.9638 (m) cc_final: 0.9351 (p) REVERT: TI 52 GLU cc_start: 0.8810 (tt0) cc_final: 0.8403 (mt-10) REVERT: TA 97 ILE cc_start: 0.9593 (pt) cc_final: 0.9359 (pp) REVERT: TA 114 MET cc_start: 0.9070 (ttp) cc_final: 0.8805 (ptm) REVERT: TA 131 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8542 (mppt) REVERT: TA 155 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (tp30) REVERT: TA 171 ASP cc_start: 0.9115 (t0) cc_final: 0.8668 (t0) REVERT: TA 194 ASP cc_start: 0.8307 (t70) cc_final: 0.7334 (t0) REVERT: TA 222 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8387 (tp30) REVERT: TA 251 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8970 (mt-10) REVERT: TA 280 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8760 (mt-10) REVERT: TA 319 MET cc_start: 0.8840 (tmm) cc_final: 0.8618 (tmm) REVERT: TA 352 CYS cc_start: 0.8639 (t) cc_final: 0.7905 (t) REVERT: TA 360 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8951 (tp30) REVERT: TA 367 ASP cc_start: 0.9039 (m-30) cc_final: 0.8791 (m-30) REVERT: TA 372 ASN cc_start: 0.9103 (m-40) cc_final: 0.8344 (m-40) REVERT: TA 389 MET cc_start: 0.9122 (mtt) cc_final: 0.8719 (mtm) REVERT: TB 22 SER cc_start: 0.9292 (t) cc_final: 0.8817 (p) REVERT: TB 65 TRP cc_start: 0.8315 (m-90) cc_final: 0.7794 (m-90) REVERT: TB 138 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8343 (p0) REVERT: TB 171 ASP cc_start: 0.9442 (t0) cc_final: 0.8698 (p0) REVERT: TB 194 ASP cc_start: 0.8476 (m-30) cc_final: 0.8206 (m-30) REVERT: TB 251 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8859 (mt-10) REVERT: TB 254 ASP cc_start: 0.9436 (m-30) cc_final: 0.9192 (m-30) REVERT: TB 272 ASP cc_start: 0.8543 (p0) cc_final: 0.7908 (p0) REVERT: TB 328 TRP cc_start: 0.9223 (m100) cc_final: 0.8711 (m100) REVERT: TB 362 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8485 (mm-30) REVERT: LA 192 MET cc_start: 0.9319 (tpt) cc_final: 0.7828 (tpp) REVERT: LA 281 ASN cc_start: 0.7909 (t0) cc_final: 0.7660 (t0) REVERT: LA 310 MET cc_start: 0.9632 (mtp) cc_final: 0.9397 (mmt) REVERT: LA 337 ASP cc_start: 0.8951 (m-30) cc_final: 0.8578 (m-30) REVERT: LA 361 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8094 (tp30) REVERT: LA 363 LYS cc_start: 0.8977 (mttt) cc_final: 0.8479 (mtpp) REVERT: LB 119 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8831 (pm20) REVERT: LB 126 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8246 (pm20) REVERT: LB 192 MET cc_start: 0.9433 (tpt) cc_final: 0.7367 (mtt) REVERT: LB 202 GLU cc_start: 0.9016 (tp30) cc_final: 0.8723 (tp30) REVERT: LF 153 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8532 (mt-10) REVERT: LF 192 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5462 (mmt) REVERT: LF 202 GLU cc_start: 0.9051 (tt0) cc_final: 0.8369 (tp30) REVERT: LF 206 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8633 (mm-40) REVERT: LF 337 ASP cc_start: 0.9143 (m-30) cc_final: 0.8512 (m-30) REVERT: LF 358 GLN cc_start: 0.8657 (tp40) cc_final: 0.8412 (mp10) REVERT: LF 361 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: LF 365 TYR cc_start: 0.9347 (p90) cc_final: 0.8879 (p90) REVERT: LE 105 ASP cc_start: 0.8802 (t70) cc_final: 0.8568 (t0) REVERT: LE 122 MET cc_start: 0.9547 (mmt) cc_final: 0.9165 (mmm) REVERT: LE 192 MET cc_start: 0.8845 (tpt) cc_final: 0.7097 (mtt) REVERT: LE 361 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8836 (tt0) REVERT: LD 105 ASP cc_start: 0.8348 (m-30) cc_final: 0.7639 (t0) REVERT: LD 192 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6740 (mtt) REVERT: LD 253 LYS cc_start: 0.9349 (ttpt) cc_final: 0.9107 (ttmm) REVERT: LD 287 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8632 (mm-30) REVERT: LD 361 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8743 (tt0) REVERT: LD 367 ASP cc_start: 0.8995 (t0) cc_final: 0.8732 (t0) REVERT: LC 171 THR cc_start: 0.9078 (m) cc_final: 0.8706 (p) REVERT: LC 192 MET cc_start: 0.9266 (tpt) cc_final: 0.7437 (mtt) REVERT: LC 197 MET cc_start: 0.9023 (mmm) cc_final: 0.8316 (mpt) REVERT: LC 290 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8516 (mtm-85) REVERT: LC 358 GLN cc_start: 0.8768 (tt0) cc_final: 0.8427 (pm20) REVERT: LC 366 GLU cc_start: 0.8999 (mp0) cc_final: 0.8786 (mm-30) outliers start: 43 outliers final: 24 residues processed: 568 average time/residue: 1.3857 time to fit residues: 928.4237 Evaluate side-chains 554 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 521 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TE residue 78 ILE Chi-restraints excluded: chain TF residue 5 ILE 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 155 GLU Chi-restraints excluded: chain TA residue 180 VAL Chi-restraints excluded: chain TA residue 222 GLU Chi-restraints excluded: chain TA residue 254 ASP Chi-restraints excluded: chain TB residue 48 LEU 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 247 LEU 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 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 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 290 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 54 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 87 optimal weight: 0.0970 chunk 326 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 345 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 105 GLN TE 83 GLN TF 31 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 31 GLN TG 80 GLN TI 31 GLN TI 83 GLN TB 138 ASN TB 205 GLN ** 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 136 ASN LE 376 ASN LD 356 ASN ** LC 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.069683 restraints weight = 51205.970| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.44 r_work: 0.2718 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28662 Z= 0.111 Angle : 0.558 10.378 38989 Z= 0.294 Chirality : 0.045 0.215 4385 Planarity : 0.003 0.047 5287 Dihedral : 5.639 70.386 4027 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 21.23 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3635 helix: 1.61 (0.20), residues: 740 sheet: 0.25 (0.16), residues: 1026 loop : -0.71 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPTC 65 HIS 0.003 0.001 HISTB 266 PHE 0.019 0.001 PHETA 252 TYR 0.025 0.001 TYRTC 290 ARG 0.011 0.000 ARGLB 193 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 820) hydrogen bonds : angle 5.28114 ( 2304) metal coordination : bond 0.00045 ( 6) covalent geometry : bond 0.00250 (28656) covalent geometry : angle 0.55842 (38989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28840.93 seconds wall clock time: 506 minutes 27.03 seconds (30387.03 seconds total)