Starting phenix.real_space_refine on Sat Oct 11 12:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpg_18550/10_2025/8qpg_18550.map" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 21 5.21 5 S 24 5.16 5 C 8895 2.51 5 N 2451 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14550 Number of models: 1 Model: "" Number of chains: 18 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: "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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "TE" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "TF" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "TG" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "TH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "TI" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 4.00, per 1000 atoms: 0.27 Number of scatterers: 14550 At special positions: 0 Unit cell: (101.877, 99.535, 122.955, 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 24 16.00 P 6 15.00 Mg 21 11.99 O 3150 8.00 N 2451 7.00 C 8895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 612.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNTA 501 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 270 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 266 " pdb=" ZNTB 501 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 270 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 266 " pdb=" ZNTC 501 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 270 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 266 " 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 23 sheets defined 18.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... 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 236 through 240 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 removed outlier: 3.773A pdb=" N ALATC 337 " --> pdb=" O GLUTC 333 " (cutoff:3.500A) No H-bonds generated for '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 412 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 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 236 through 240 Processing helix chain 'TA' and resid 248 through 257 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: 3.789A 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 412 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 257 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: 3.774A 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 413 removed outlier: 3.717A pdb=" N GLNTB 413 " --> pdb=" O PHETB 409 " (cutoff:3.500A) 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 55 WARNING: can't find start of bonding for strands! previous: chain 'TC' and resid 54 through 55 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: 7.279A pdb=" N TRPTC 65 " --> pdb=" O SERTC 100 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SERTC 100 " --> pdb=" O TRPTC 65 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ALATC 67 " --> pdb=" O ARGTC 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARGTC 98 " --> pdb=" O ALATC 67 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLNTC 176 " --> pdb=" O PHETC 101 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SERTC 145 " --> pdb=" O PHETC 163 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHETC 163 " --> pdb=" O SERTC 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'TC' and resid 204 through 211 removed outlier: 6.416A pdb=" N HISTC 304 " --> pdb=" O ALATC 263 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRPTC 328 " --> pdb=" O TYRTC 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'TC' and resid 326 through 331 current: chain 'TC' and resid 373 through 379 Processing sheet with id=AA5, first strand: chain 'TD' and resid 3 through 9 removed outlier: 4.234A pdb=" N ASPTE 3 " --> pdb=" O THRTD 4 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASPTF 3 " --> pdb=" O THRTE 4 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASPTG 3 " --> pdb=" O THRTF 4 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASPTH 3 " --> pdb=" O THRTG 4 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASPTI 3 " --> pdb=" O THRTH 4 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASPTD 3 " --> pdb=" O VALTI 6 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VALTI 8 " --> pdb=" O ASPTD 3 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILETD 5 " --> pdb=" O VALTI 8 " (cutoff:3.500A) Processing sheet with id=AA6, 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 77 through 79 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'TD' and resid 25 through 28 removed outlier: 3.571A pdb=" N ASPTD 71 " --> pdb=" O VALTD 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUTD 53 " --> pdb=" O THRTD 69 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THRTD 69 " --> pdb=" O LEUTD 53 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THRTD 55 " --> pdb=" O ALATD 67 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALATD 67 " --> pdb=" O THRTD 55 " (cutoff:3.500A) Processing sheet with id=AA8, 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 77 through 79 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'TE' and resid 25 through 28 removed outlier: 3.569A pdb=" N ASPTE 71 " --> pdb=" O VALTE 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUTE 53 " --> pdb=" O THRTE 69 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THRTE 69 " --> pdb=" O LEUTE 53 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THRTE 55 " --> pdb=" O ALATE 67 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALATE 67 " --> pdb=" O THRTE 55 " (cutoff:3.500A) Processing sheet with id=AB1, 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 77 through 79 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'TF' and resid 25 through 28 removed outlier: 3.572A pdb=" N ASPTF 71 " --> pdb=" O VALTF 51 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEUTF 53 " --> pdb=" O THRTF 69 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THRTF 69 " --> pdb=" O LEUTF 53 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THRTF 55 " --> pdb=" O ALATF 67 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALATF 67 " --> pdb=" O THRTF 55 " (cutoff:3.500A) Processing sheet with id=AB3, 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 77 through 79 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'TG' and resid 25 through 28 removed outlier: 3.567A pdb=" N ASPTG 71 " --> pdb=" O VALTG 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUTG 53 " --> pdb=" O THRTG 69 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THRTG 69 " --> pdb=" O LEUTG 53 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THRTG 55 " --> pdb=" O ALATG 67 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALATG 67 " --> pdb=" O THRTG 55 " (cutoff:3.500A) Processing sheet with id=AB5, 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 77 through 79 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'TH' and resid 25 through 28 removed outlier: 3.573A pdb=" N ASPTH 71 " --> pdb=" O VALTH 51 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEUTH 53 " --> pdb=" O THRTH 69 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THRTH 69 " --> pdb=" O LEUTH 53 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THRTH 55 " --> pdb=" O ALATH 67 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALATH 67 " --> pdb=" O THRTH 55 " (cutoff:3.500A) Processing sheet with id=AB7, 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 77 through 79 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'TI' and resid 25 through 28 removed outlier: 3.568A pdb=" N ASPTI 71 " --> pdb=" O VALTI 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUTI 53 " --> pdb=" O THRTI 69 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THRTI 69 " --> pdb=" O LEUTI 53 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THRTI 55 " --> pdb=" O ALATI 67 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALATI 67 " --> pdb=" O THRTI 55 " (cutoff:3.500A) Processing sheet with id=AB9, 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=AB9 Processing sheet with id=AC1, first strand: chain 'TA' and resid 65 through 69 removed outlier: 6.487A pdb=" N ASPTA 96 " --> pdb=" O ASNTA 68 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLNTA 176 " --> pdb=" O PHETA 101 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SERTA 145 " --> pdb=" O PHETA 163 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHETA 163 " --> pdb=" O SERTA 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'TA' and resid 204 through 211 removed outlier: 6.411A pdb=" N HISTA 304 " --> pdb=" O ALATA 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRPTA 328 " --> pdb=" O TYRTA 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'TA' and resid 326 through 331 current: chain 'TA' and resid 373 through 379 Processing sheet with id=AC3, 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=AC3 Processing sheet with id=AC4, first strand: chain 'TB' and resid 65 through 69 removed outlier: 7.282A pdb=" N TRPTB 65 " --> pdb=" O SERTB 100 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SERTB 100 " --> pdb=" O TRPTB 65 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALATB 67 " --> pdb=" O ARGTB 98 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARGTB 98 " --> pdb=" O ALATB 67 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLNTB 176 " --> pdb=" O PHETB 101 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N SERTB 145 " --> pdb=" O PHETB 163 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHETB 163 " --> pdb=" O SERTB 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'TB' and resid 204 through 211 removed outlier: 6.437A pdb=" N HISTB 304 " --> pdb=" O ALATB 263 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRPTB 328 " --> pdb=" O TYRTB 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'TB' and resid 326 through 331 current: chain 'TB' and resid 374 through 379 402 hydrogen bonds defined for protein. 1110 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: 2.50 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3785 1.34 - 1.46: 4256 1.46 - 1.58: 6665 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 14754 Sorted by residual: bond pdb=" NE2 NEPTG 45 " pdb=" P NEPTG 45 " ideal model delta sigma weight residual 1.850 1.746 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" NE2 NEPTH 45 " pdb=" P NEPTH 45 " ideal model delta sigma weight residual 1.850 1.746 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" NE2 NEPTI 45 " pdb=" P NEPTI 45 " ideal model delta sigma weight residual 1.850 1.747 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" NE2 NEPTF 45 " pdb=" P NEPTF 45 " ideal model delta sigma weight residual 1.850 1.747 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" NE2 NEPTE 45 " pdb=" P NEPTE 45 " ideal model delta sigma weight residual 1.850 1.747 0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 14749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 18566 2.70 - 5.40: 1393 5.40 - 8.11: 120 8.11 - 10.81: 10 10.81 - 13.51: 5 Bond angle restraints: 20094 Sorted by residual: angle pdb=" CA ASPTA 27 " pdb=" CB ASPTA 27 " pdb=" CG ASPTA 27 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.00e+00 1.00e+00 5.34e+01 angle pdb=" CA HISTC 266 " pdb=" CB HISTC 266 " pdb=" CG HISTC 266 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.01e+01 angle pdb=" CA HISTB 266 " pdb=" CB HISTB 266 " pdb=" CG HISTB 266 " ideal model delta sigma weight residual 113.80 120.62 -6.82 1.00e+00 1.00e+00 4.65e+01 angle pdb=" CA HISTA 266 " pdb=" CB HISTA 266 " pdb=" CG HISTA 266 " ideal model delta sigma weight residual 113.80 120.50 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" C ARGTA 133 " pdb=" CA ARGTA 133 " pdb=" CB ARGTA 133 " ideal model delta sigma weight residual 110.14 119.77 -9.63 1.54e+00 4.22e-01 3.91e+01 ... (remaining 20089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8035 18.00 - 35.99: 480 35.99 - 53.99: 98 53.99 - 71.99: 48 71.99 - 89.98: 27 Dihedral angle restraints: 8688 sinusoidal: 3201 harmonic: 5487 Sorted by residual: dihedral pdb=" CA ARGTB 298 " pdb=" C ARGTB 298 " pdb=" N GLUTB 299 " pdb=" CA GLUTB 299 " ideal model delta harmonic sigma weight residual -180.00 -149.25 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" C ASPTC 212 " pdb=" N ASPTC 212 " pdb=" CA ASPTC 212 " pdb=" CB ASPTC 212 " ideal model delta harmonic sigma weight residual -122.60 -137.69 15.09 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" CA ARGTA 298 " pdb=" C ARGTA 298 " pdb=" N GLUTA 299 " pdb=" CA GLUTA 299 " ideal model delta harmonic sigma weight residual -180.00 -150.06 -29.94 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 8685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1507 0.103 - 0.206: 657 0.206 - 0.310: 129 0.310 - 0.413: 23 0.413 - 0.516: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CA ASPTB 212 " pdb=" N ASPTB 212 " pdb=" C ASPTB 212 " pdb=" CB ASPTB 212 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA ASPTC 212 " pdb=" N ASPTC 212 " pdb=" C ASPTC 212 " pdb=" CB ASPTC 212 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CA ASPTA 212 " pdb=" N ASPTA 212 " pdb=" C ASPTA 212 " pdb=" CB ASPTA 212 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 2316 not shown) Planarity restraints: 2685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRTA 305 " -0.087 2.00e-02 2.50e+03 4.45e-02 3.96e+01 pdb=" CG TYRTA 305 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYRTA 305 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYRTA 305 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYRTA 305 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYRTA 305 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYRTA 305 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYRTA 305 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRTA 290 " 0.084 2.00e-02 2.50e+03 4.25e-02 3.61e+01 pdb=" CG TYRTA 290 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYRTA 290 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYRTA 290 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYRTA 290 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYRTA 290 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRTA 290 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYRTA 290 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRTB 305 " -0.082 2.00e-02 2.50e+03 4.18e-02 3.49e+01 pdb=" CG TYRTB 305 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYRTB 305 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYRTB 305 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYRTB 305 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYRTB 305 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYRTB 305 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYRTB 305 " -0.047 2.00e-02 2.50e+03 ... (remaining 2682 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 60 2.44 - 3.05: 9313 3.05 - 3.67: 23448 3.67 - 4.28: 38497 4.28 - 4.90: 62500 Nonbonded interactions: 133818 Sorted by model distance: nonbonded pdb=" OD2 ASPTA 212 " pdb="ZN ZNTA 501 " model vdw 1.825 2.230 nonbonded pdb=" OD2 ASPTB 212 " pdb="ZN ZNTB 501 " model vdw 1.845 2.230 nonbonded pdb=" OD2 ASPTC 212 " pdb="ZN ZNTC 501 " model vdw 1.862 2.230 nonbonded pdb=" OE2 GLUTC 60 " pdb="MG MGTC 502 " model vdw 1.913 2.170 nonbonded pdb=" OE2 GLUTB 60 " pdb="MG MGTB 502 " model vdw 1.917 2.170 ... (remaining 133813 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: 0.01 Found NCS groups: ncs_group { reference = chain 'TA' selection = chain 'TB' selection = chain 'TC' } ncs_group { reference = chain 'TD' selection = chain 'TE' selection = chain 'TF' selection = chain 'TG' selection = chain 'TH' selection = chain 'TI' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.430 14760 Z= 0.607 Angle : 1.500 13.510 20094 Z= 0.953 Chirality : 0.113 0.516 2319 Planarity : 0.009 0.111 2685 Dihedral : 14.873 89.984 5172 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.31 % Allowed : 2.26 % Favored : 97.42 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 1884 helix: -0.01 (0.27), residues: 258 sheet: 0.56 (0.20), residues: 642 loop : -1.09 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARGTA 118 TYR 0.087 0.013 TYRTA 305 PHE 0.049 0.010 PHETA 354 TRP 0.057 0.018 TRPTB 156 HIS 0.019 0.005 HISTA 214 Details of bonding type rmsd covalent geometry : bond 0.00825 (14754) covalent geometry : angle 1.49983 (20094) hydrogen bonds : bond 0.13387 ( 402) hydrogen bonds : angle 6.79728 ( 1110) metal coordination : bond 0.40976 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 0.690 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8520 (t0) cc_final: 0.8083 (t0) REVERT: TC 194 ASP cc_start: 0.8793 (t70) cc_final: 0.8342 (t70) REVERT: TC 408 ASP cc_start: 0.8675 (t0) cc_final: 0.8463 (t0) REVERT: TD 55 THR cc_start: 0.9522 (m) cc_final: 0.9198 (p) REVERT: TD 59 ASP cc_start: 0.8937 (m-30) cc_final: 0.8433 (t0) REVERT: TD 63 VAL cc_start: 0.9722 (t) cc_final: 0.9487 (m) REVERT: TD 71 ASP cc_start: 0.8857 (t0) cc_final: 0.8579 (t0) REVERT: TD 83 GLN cc_start: 0.8884 (mt0) cc_final: 0.8604 (tt0) REVERT: TD 92 THR cc_start: 0.9490 (m) cc_final: 0.9209 (p) REVERT: TE 55 THR cc_start: 0.9348 (m) cc_final: 0.9068 (p) REVERT: TE 59 ASP cc_start: 0.9008 (m-30) cc_final: 0.8669 (t0) REVERT: TE 63 VAL cc_start: 0.9416 (t) cc_final: 0.9135 (m) REVERT: TE 92 THR cc_start: 0.9438 (m) cc_final: 0.9129 (p) REVERT: TF 29 ASP cc_start: 0.8945 (t0) cc_final: 0.8670 (t0) REVERT: TF 55 THR cc_start: 0.9500 (m) cc_final: 0.9250 (p) REVERT: TF 59 ASP cc_start: 0.9039 (m-30) cc_final: 0.8760 (t70) REVERT: TF 63 VAL cc_start: 0.9710 (t) cc_final: 0.9500 (m) REVERT: TF 83 GLN cc_start: 0.8966 (mt0) cc_final: 0.8702 (mt0) REVERT: TF 92 THR cc_start: 0.9492 (m) cc_final: 0.9276 (p) REVERT: TF 112 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8405 (mt-10) REVERT: TG 55 THR cc_start: 0.9420 (m) cc_final: 0.9117 (p) REVERT: TG 58 ASP cc_start: 0.8894 (t70) cc_final: 0.8631 (t0) REVERT: TG 59 ASP cc_start: 0.8978 (m-30) cc_final: 0.8541 (t0) REVERT: TG 63 VAL cc_start: 0.9466 (t) cc_final: 0.9184 (m) REVERT: TG 65 ASP cc_start: 0.8426 (t0) cc_final: 0.8066 (t0) REVERT: TG 71 ASP cc_start: 0.9045 (t0) cc_final: 0.8740 (t0) REVERT: TG 92 THR cc_start: 0.9534 (m) cc_final: 0.9216 (p) REVERT: TH 55 THR cc_start: 0.9572 (m) cc_final: 0.9252 (p) REVERT: TH 59 ASP cc_start: 0.8936 (m-30) cc_final: 0.8542 (t0) REVERT: TH 63 VAL cc_start: 0.9695 (t) cc_final: 0.9442 (m) REVERT: TH 83 GLN cc_start: 0.8903 (mt0) cc_final: 0.8464 (mt0) REVERT: TH 92 THR cc_start: 0.9423 (m) cc_final: 0.9153 (p) REVERT: TI 29 ASP cc_start: 0.8843 (t0) cc_final: 0.8492 (t0) REVERT: TI 55 THR cc_start: 0.9432 (m) cc_final: 0.9127 (p) REVERT: TI 59 ASP cc_start: 0.8968 (m-30) cc_final: 0.8586 (t0) REVERT: TI 63 VAL cc_start: 0.9415 (t) cc_final: 0.9120 (m) REVERT: TI 92 THR cc_start: 0.9528 (m) cc_final: 0.9256 (p) REVERT: TI 112 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8504 (mt-10) REVERT: TA 408 ASP cc_start: 0.8683 (t0) cc_final: 0.8357 (t0) REVERT: TB 7 ASP cc_start: 0.8662 (t0) cc_final: 0.8387 (t0) REVERT: TB 194 ASP cc_start: 0.8848 (t70) cc_final: 0.8471 (t70) REVERT: TB 319 MET cc_start: 0.8881 (tmm) cc_final: 0.8607 (tmm) outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 0.4499 time to fit residues: 269.3070 Evaluate side-chains 416 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 183 ASN TC 214 HIS TC 260 HIS TC 324 HIS TD 31 GLN TD 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TG 83 GLN TH 31 GLN TA 183 ASN TA 260 HIS TA 324 HIS TA 349 ASN TB 183 ASN TB 260 HIS TB 324 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.069083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.058169 restraints weight = 24501.501| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 2.28 r_work: 0.2390 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2270 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14760 Z= 0.175 Angle : 0.558 6.179 20094 Z= 0.316 Chirality : 0.047 0.151 2319 Planarity : 0.003 0.042 2685 Dihedral : 6.716 55.771 2067 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.64 % Allowed : 10.31 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 1884 helix: 1.58 (0.30), residues: 261 sheet: 0.58 (0.20), residues: 669 loop : -0.66 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGTB 52 TYR 0.027 0.002 TYRTB 290 PHE 0.021 0.002 PHETA 354 TRP 0.009 0.001 TRPTC 65 HIS 0.005 0.001 HISTA 324 Details of bonding type rmsd covalent geometry : bond 0.00384 (14754) covalent geometry : angle 0.55786 (20094) hydrogen bonds : bond 0.04267 ( 402) hydrogen bonds : angle 5.13971 ( 1110) metal coordination : bond 0.00547 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 390 time to evaluate : 0.606 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8740 (t0) cc_final: 0.8255 (t0) REVERT: TC 22 SER cc_start: 0.9194 (t) cc_final: 0.8774 (m) REVERT: TC 89 THR cc_start: 0.9122 (m) cc_final: 0.8627 (p) REVERT: TC 199 ASP cc_start: 0.8922 (t0) cc_final: 0.8712 (t0) REVERT: TD 55 THR cc_start: 0.9318 (m) cc_final: 0.9009 (t) REVERT: TD 58 ASP cc_start: 0.8627 (t70) cc_final: 0.8236 (t0) REVERT: TD 63 VAL cc_start: 0.9300 (t) cc_final: 0.8872 (m) REVERT: TD 65 ASP cc_start: 0.8987 (t0) cc_final: 0.8768 (t0) REVERT: TD 71 ASP cc_start: 0.9076 (t0) cc_final: 0.8789 (t0) REVERT: TD 83 GLN cc_start: 0.9068 (mt0) cc_final: 0.8435 (mt0) REVERT: TD 85 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8656 (mt-10) REVERT: TD 92 THR cc_start: 0.9542 (m) cc_final: 0.8949 (p) REVERT: TE 24 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8444 (mt-10) REVERT: TE 58 ASP cc_start: 0.8872 (t0) cc_final: 0.8632 (t0) REVERT: TE 59 ASP cc_start: 0.9297 (m-30) cc_final: 0.8649 (t0) REVERT: TE 64 GLU cc_start: 0.8631 (tt0) cc_final: 0.8169 (tm-30) REVERT: TE 92 THR cc_start: 0.9553 (m) cc_final: 0.9038 (p) REVERT: TF 29 ASP cc_start: 0.9007 (t0) cc_final: 0.8728 (t0) REVERT: TF 39 GLU cc_start: 0.9001 (tt0) cc_final: 0.8450 (tt0) REVERT: TF 58 ASP cc_start: 0.8565 (t0) cc_final: 0.8051 (t0) REVERT: TF 59 ASP cc_start: 0.9233 (m-30) cc_final: 0.8647 (t70) REVERT: TF 61 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8622 (mt-10) REVERT: TF 63 VAL cc_start: 0.9319 (t) cc_final: 0.8990 (m) REVERT: TF 83 GLN cc_start: 0.9080 (mt0) cc_final: 0.8477 (tt0) REVERT: TF 92 THR cc_start: 0.9580 (m) cc_final: 0.9112 (p) REVERT: TF 112 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8569 (mt-10) REVERT: TG 39 GLU cc_start: 0.8966 (tt0) cc_final: 0.8548 (tt0) REVERT: TG 58 ASP cc_start: 0.8834 (t70) cc_final: 0.8362 (t0) REVERT: TG 63 VAL cc_start: 0.9066 (t) cc_final: 0.8594 (m) REVERT: TG 71 ASP cc_start: 0.9005 (t0) cc_final: 0.8656 (t0) REVERT: TG 83 GLN cc_start: 0.8898 (tt0) cc_final: 0.8506 (tt0) REVERT: TG 92 THR cc_start: 0.9610 (m) cc_final: 0.9166 (p) REVERT: TH 52 GLU cc_start: 0.9088 (tt0) cc_final: 0.8749 (tt0) REVERT: TH 58 ASP cc_start: 0.8631 (t0) cc_final: 0.8380 (t0) REVERT: TH 59 ASP cc_start: 0.9270 (m-30) cc_final: 0.8698 (t0) REVERT: TH 83 GLN cc_start: 0.8982 (mt0) cc_final: 0.8496 (tt0) REVERT: TH 92 THR cc_start: 0.9548 (m) cc_final: 0.9139 (p) REVERT: TI 5 ILE cc_start: 0.9392 (mt) cc_final: 0.9188 (mp) REVERT: TI 29 ASP cc_start: 0.8838 (t0) cc_final: 0.8552 (t0) REVERT: TI 58 ASP cc_start: 0.8747 (t0) cc_final: 0.8545 (t0) REVERT: TI 59 ASP cc_start: 0.9132 (m-30) cc_final: 0.8662 (t0) REVERT: TI 63 VAL cc_start: 0.9092 (t) cc_final: 0.8613 (m) REVERT: TI 83 GLN cc_start: 0.9027 (mt0) cc_final: 0.8627 (tt0) REVERT: TI 92 THR cc_start: 0.9606 (m) cc_final: 0.9126 (p) REVERT: TI 112 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8795 (mt-10) REVERT: TA 22 SER cc_start: 0.9175 (t) cc_final: 0.8861 (m) REVERT: TA 24 SER cc_start: 0.9048 (m) cc_final: 0.8807 (t) REVERT: TA 38 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8950 (mpp80) REVERT: TA 69 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8891 (tp) REVERT: TA 89 THR cc_start: 0.9149 (m) cc_final: 0.8707 (p) REVERT: TA 116 LEU cc_start: 0.9067 (tt) cc_final: 0.8775 (tt) REVERT: TB 7 ASP cc_start: 0.8749 (t0) cc_final: 0.8502 (t0) REVERT: TB 19 SER cc_start: 0.9156 (t) cc_final: 0.8857 (p) REVERT: TB 24 SER cc_start: 0.9137 (m) cc_final: 0.8833 (t) REVERT: TB 89 THR cc_start: 0.9131 (m) cc_final: 0.8717 (p) REVERT: TB 189 ASP cc_start: 0.9048 (t0) cc_final: 0.8833 (t0) REVERT: TB 315 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8822 (mt-10) REVERT: TB 319 MET cc_start: 0.9444 (tmm) cc_final: 0.9126 (tmm) outliers start: 42 outliers final: 13 residues processed: 411 average time/residue: 0.4972 time to fit residues: 229.8028 Evaluate side-chains 362 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 347 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 81 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TE residue 27 LEU Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TA residue 38 ARG Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 81 VAL Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN TD 42 ASN TD 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 31 GLN TE 42 ASN TF 80 GLN TH 31 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.068006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.057362 restraints weight = 24877.074| |-----------------------------------------------------------------------------| r_work (start): 0.2474 rms_B_bonded: 2.22 r_work: 0.2347 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2229 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14760 Z= 0.259 Angle : 0.558 6.988 20094 Z= 0.310 Chirality : 0.046 0.161 2319 Planarity : 0.004 0.041 2685 Dihedral : 6.411 55.582 2067 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 11.13 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1884 helix: 1.78 (0.31), residues: 264 sheet: 0.26 (0.21), residues: 672 loop : -0.63 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGTB 52 TYR 0.027 0.002 TYRTB 290 PHE 0.021 0.002 PHETB 354 TRP 0.010 0.002 TRPTC 65 HIS 0.006 0.001 HISTB 304 Details of bonding type rmsd covalent geometry : bond 0.00579 (14754) covalent geometry : angle 0.55799 (20094) hydrogen bonds : bond 0.04009 ( 402) hydrogen bonds : angle 5.00708 ( 1110) metal coordination : bond 0.00455 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 0.604 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8564 (t0) cc_final: 0.8059 (t0) REVERT: TC 22 SER cc_start: 0.9204 (t) cc_final: 0.8746 (m) REVERT: TC 89 THR cc_start: 0.9135 (m) cc_final: 0.8690 (p) REVERT: TC 217 ASP cc_start: 0.9292 (m-30) cc_final: 0.8795 (m-30) REVERT: TD 58 ASP cc_start: 0.8666 (t70) cc_final: 0.8193 (t0) REVERT: TD 63 VAL cc_start: 0.9243 (t) cc_final: 0.8713 (m) REVERT: TD 83 GLN cc_start: 0.9063 (mt0) cc_final: 0.8593 (mt0) REVERT: TD 85 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8798 (mt-10) REVERT: TD 92 THR cc_start: 0.9524 (m) cc_final: 0.9021 (p) REVERT: TD 111 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8711 (mtt90) REVERT: TE 24 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8524 (mt-10) REVERT: TE 58 ASP cc_start: 0.8900 (t0) cc_final: 0.8608 (t0) REVERT: TE 59 ASP cc_start: 0.9283 (m-30) cc_final: 0.8773 (t0) REVERT: TE 64 GLU cc_start: 0.8849 (tt0) cc_final: 0.8320 (tm-30) REVERT: TE 83 GLN cc_start: 0.9227 (tt0) cc_final: 0.8591 (tt0) REVERT: TE 92 THR cc_start: 0.9514 (m) cc_final: 0.9023 (p) REVERT: TF 29 ASP cc_start: 0.9084 (t0) cc_final: 0.8796 (t0) REVERT: TF 58 ASP cc_start: 0.8588 (t0) cc_final: 0.7962 (t0) REVERT: TF 59 ASP cc_start: 0.9184 (m-30) cc_final: 0.8648 (t70) REVERT: TF 61 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8549 (mt-10) REVERT: TF 83 GLN cc_start: 0.9096 (mt0) cc_final: 0.8646 (tt0) REVERT: TF 112 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8531 (mt-10) REVERT: TG 29 ASP cc_start: 0.8800 (t0) cc_final: 0.8590 (t0) REVERT: TG 39 GLU cc_start: 0.9051 (tt0) cc_final: 0.8702 (tt0) REVERT: TG 58 ASP cc_start: 0.8850 (t70) cc_final: 0.8306 (t70) REVERT: TG 92 THR cc_start: 0.9610 (m) cc_final: 0.9139 (p) REVERT: TH 58 ASP cc_start: 0.8658 (t0) cc_final: 0.8323 (t0) REVERT: TH 59 ASP cc_start: 0.9247 (m-30) cc_final: 0.8766 (t0) REVERT: TH 83 GLN cc_start: 0.8995 (mt0) cc_final: 0.8543 (mt0) REVERT: TH 92 THR cc_start: 0.9608 (m) cc_final: 0.9152 (p) REVERT: TI 29 ASP cc_start: 0.8910 (t0) cc_final: 0.8677 (t0) REVERT: TI 58 ASP cc_start: 0.8797 (t0) cc_final: 0.8459 (t0) REVERT: TI 59 ASP cc_start: 0.9174 (m-30) cc_final: 0.8642 (t0) REVERT: TI 65 ASP cc_start: 0.9139 (t0) cc_final: 0.8922 (t0) REVERT: TI 83 GLN cc_start: 0.9079 (mt0) cc_final: 0.8700 (tp40) REVERT: TI 92 THR cc_start: 0.9571 (m) cc_final: 0.9102 (p) REVERT: TI 112 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8711 (mt-10) REVERT: TA 22 SER cc_start: 0.9111 (t) cc_final: 0.8723 (m) REVERT: TA 24 SER cc_start: 0.9063 (m) cc_final: 0.8827 (t) REVERT: TA 89 THR cc_start: 0.9166 (m) cc_final: 0.8697 (p) REVERT: TA 189 ASP cc_start: 0.9099 (t70) cc_final: 0.8867 (t0) REVERT: TB 19 SER cc_start: 0.9201 (t) cc_final: 0.8900 (p) REVERT: TB 24 SER cc_start: 0.9158 (m) cc_final: 0.8858 (t) REVERT: TB 27 ASP cc_start: 0.9013 (p0) cc_final: 0.8760 (p0) REVERT: TB 54 THR cc_start: 0.9481 (m) cc_final: 0.9210 (p) REVERT: TB 89 THR cc_start: 0.9131 (m) cc_final: 0.8706 (p) REVERT: TB 189 ASP cc_start: 0.9039 (t0) cc_final: 0.8717 (t0) REVERT: TB 319 MET cc_start: 0.9418 (tmm) cc_final: 0.9141 (tmm) outliers start: 47 outliers final: 22 residues processed: 379 average time/residue: 0.5395 time to fit residues: 227.7957 Evaluate side-chains 356 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 164 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 38 ILE Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 112 GLU Chi-restraints excluded: chain TE residue 38 ILE Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 164 GLU Chi-restraints excluded: chain TB residue 81 VAL Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 188 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 80 GLN TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.066938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.056063 restraints weight = 24916.735| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.26 r_work: 0.2361 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14760 Z= 0.226 Angle : 0.528 5.966 20094 Z= 0.293 Chirality : 0.046 0.153 2319 Planarity : 0.003 0.040 2685 Dihedral : 6.226 55.364 2067 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.64 % Allowed : 13.21 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 1884 helix: 1.93 (0.32), residues: 264 sheet: 0.16 (0.21), residues: 666 loop : -0.60 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGTB 52 TYR 0.026 0.002 TYRTB 290 PHE 0.019 0.002 PHETB 354 TRP 0.008 0.001 TRPTC 65 HIS 0.005 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00504 (14754) covalent geometry : angle 0.52757 (20094) hydrogen bonds : bond 0.03732 ( 402) hydrogen bonds : angle 4.90687 ( 1110) metal coordination : bond 0.00371 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 351 time to evaluate : 0.580 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8536 (t0) cc_final: 0.8080 (t0) REVERT: TC 22 SER cc_start: 0.9155 (t) cc_final: 0.8671 (m) REVERT: TC 89 THR cc_start: 0.9110 (m) cc_final: 0.8659 (p) REVERT: TD 24 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8714 (mt-10) REVERT: TD 58 ASP cc_start: 0.8626 (t70) cc_final: 0.8079 (t70) REVERT: TD 63 VAL cc_start: 0.9187 (t) cc_final: 0.8713 (m) REVERT: TD 83 GLN cc_start: 0.9046 (mt0) cc_final: 0.8593 (mt0) REVERT: TD 85 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8479 (mt-10) REVERT: TD 111 ARG cc_start: 0.8933 (mtm-85) cc_final: 0.8711 (mtt90) REVERT: TD 112 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: TE 24 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8506 (mt-10) REVERT: TE 58 ASP cc_start: 0.8903 (t0) cc_final: 0.8618 (t0) REVERT: TE 83 GLN cc_start: 0.9182 (tt0) cc_final: 0.8514 (tt0) REVERT: TE 92 THR cc_start: 0.9451 (m) cc_final: 0.8963 (p) REVERT: TF 29 ASP cc_start: 0.9041 (t0) cc_final: 0.8818 (t0) REVERT: TF 58 ASP cc_start: 0.8532 (t0) cc_final: 0.7831 (t0) REVERT: TF 59 ASP cc_start: 0.9158 (m-30) cc_final: 0.8569 (t70) REVERT: TF 61 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8566 (mt-10) REVERT: TF 83 GLN cc_start: 0.9071 (mt0) cc_final: 0.8591 (tt0) REVERT: TF 112 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8479 (mt-10) REVERT: TG 39 GLU cc_start: 0.8964 (tt0) cc_final: 0.8588 (tt0) REVERT: TG 58 ASP cc_start: 0.8822 (t70) cc_final: 0.8322 (t70) REVERT: TG 83 GLN cc_start: 0.8989 (tt0) cc_final: 0.8699 (tt0) REVERT: TG 92 THR cc_start: 0.9611 (m) cc_final: 0.9169 (p) REVERT: TH 58 ASP cc_start: 0.8667 (t0) cc_final: 0.8271 (t0) REVERT: TH 59 ASP cc_start: 0.9227 (m-30) cc_final: 0.8764 (t0) REVERT: TH 83 GLN cc_start: 0.8986 (mt0) cc_final: 0.8516 (mt0) REVERT: TH 92 THR cc_start: 0.9581 (m) cc_final: 0.9127 (p) REVERT: TI 24 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8522 (mt-10) REVERT: TI 29 ASP cc_start: 0.8886 (t0) cc_final: 0.8650 (t0) REVERT: TI 52 GLU cc_start: 0.9053 (tt0) cc_final: 0.8811 (tt0) REVERT: TI 58 ASP cc_start: 0.8779 (t0) cc_final: 0.8380 (t0) REVERT: TI 59 ASP cc_start: 0.9173 (m-30) cc_final: 0.8633 (t0) REVERT: TI 65 ASP cc_start: 0.9155 (t0) cc_final: 0.8944 (t0) REVERT: TI 83 GLN cc_start: 0.9072 (mt0) cc_final: 0.8621 (tp40) REVERT: TI 92 THR cc_start: 0.9564 (m) cc_final: 0.9117 (p) REVERT: TI 112 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8726 (mt-10) REVERT: TA 22 SER cc_start: 0.9006 (t) cc_final: 0.8614 (m) REVERT: TA 24 SER cc_start: 0.8989 (m) cc_final: 0.8724 (t) REVERT: TA 54 THR cc_start: 0.9529 (m) cc_final: 0.9167 (p) REVERT: TA 89 THR cc_start: 0.9165 (m) cc_final: 0.8691 (p) REVERT: TA 189 ASP cc_start: 0.9130 (t70) cc_final: 0.8831 (t0) REVERT: TB 24 SER cc_start: 0.9105 (m) cc_final: 0.8771 (t) REVERT: TB 54 THR cc_start: 0.9450 (m) cc_final: 0.9175 (p) REVERT: TB 89 THR cc_start: 0.9103 (m) cc_final: 0.8691 (p) REVERT: TB 189 ASP cc_start: 0.9064 (t0) cc_final: 0.8742 (t0) REVERT: TB 319 MET cc_start: 0.9407 (tmm) cc_final: 0.9125 (tmm) outliers start: 42 outliers final: 23 residues processed: 371 average time/residue: 0.5115 time to fit residues: 212.0025 Evaluate side-chains 363 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 164 GLU Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TD residue 26 LEU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 112 GLU Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 38 ILE Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TH residue 113 VAL Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 315 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 131 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 42 ASN TD 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.069180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.058350 restraints weight = 24600.025| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.25 r_work: 0.2374 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14760 Z= 0.177 Angle : 0.506 7.221 20094 Z= 0.279 Chirality : 0.045 0.151 2319 Planarity : 0.003 0.036 2685 Dihedral : 6.056 54.167 2067 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.96 % Allowed : 13.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.19), residues: 1884 helix: 2.08 (0.32), residues: 264 sheet: 0.17 (0.21), residues: 636 loop : -0.65 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGTB 52 TYR 0.025 0.002 TYRTB 290 PHE 0.018 0.001 PHETB 354 TRP 0.007 0.001 TRPTC 65 HIS 0.003 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00392 (14754) covalent geometry : angle 0.50579 (20094) hydrogen bonds : bond 0.03485 ( 402) hydrogen bonds : angle 4.79933 ( 1110) metal coordination : bond 0.00269 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 0.587 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8560 (t0) cc_final: 0.8101 (t0) REVERT: TC 22 SER cc_start: 0.9189 (t) cc_final: 0.8705 (m) REVERT: TC 89 THR cc_start: 0.9154 (m) cc_final: 0.8723 (p) REVERT: TD 24 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8685 (mt-10) REVERT: TD 58 ASP cc_start: 0.8698 (t70) cc_final: 0.8158 (t70) REVERT: TD 63 VAL cc_start: 0.9279 (t) cc_final: 0.8823 (m) REVERT: TD 83 GLN cc_start: 0.9013 (mt0) cc_final: 0.8563 (mt0) REVERT: TD 85 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8514 (mt-10) REVERT: TE 9 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8589 (tp40) REVERT: TE 24 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8491 (mt-10) REVERT: TE 58 ASP cc_start: 0.8911 (t0) cc_final: 0.8619 (t0) REVERT: TE 83 GLN cc_start: 0.9205 (tt0) cc_final: 0.8579 (tt0) REVERT: TE 92 THR cc_start: 0.9467 (m) cc_final: 0.8991 (p) REVERT: TF 29 ASP cc_start: 0.9072 (t0) cc_final: 0.8861 (t0) REVERT: TF 39 GLU cc_start: 0.8911 (tt0) cc_final: 0.8682 (tt0) REVERT: TF 58 ASP cc_start: 0.8550 (t0) cc_final: 0.7867 (t0) REVERT: TF 59 ASP cc_start: 0.9163 (m-30) cc_final: 0.8588 (t70) REVERT: TF 61 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8547 (mt-10) REVERT: TF 83 GLN cc_start: 0.9090 (mt0) cc_final: 0.8600 (mt0) REVERT: TF 85 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8464 (mt-10) REVERT: TF 112 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8488 (mt-10) REVERT: TG 39 GLU cc_start: 0.8960 (tt0) cc_final: 0.8579 (tt0) REVERT: TG 52 GLU cc_start: 0.9017 (tt0) cc_final: 0.8729 (tt0) REVERT: TG 58 ASP cc_start: 0.8851 (t70) cc_final: 0.8378 (t70) REVERT: TG 65 ASP cc_start: 0.9068 (t0) cc_final: 0.8786 (t0) REVERT: TG 92 THR cc_start: 0.9639 (m) cc_final: 0.9117 (p) REVERT: TH 24 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8588 (pt0) REVERT: TH 58 ASP cc_start: 0.8685 (t0) cc_final: 0.8252 (t70) REVERT: TH 59 ASP cc_start: 0.9239 (m-30) cc_final: 0.8780 (t0) REVERT: TH 83 GLN cc_start: 0.8959 (mt0) cc_final: 0.8544 (mt0) REVERT: TH 92 THR cc_start: 0.9600 (m) cc_final: 0.9144 (p) REVERT: TH 112 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: TI 24 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8495 (mt-10) REVERT: TI 29 ASP cc_start: 0.8911 (t0) cc_final: 0.8697 (t0) REVERT: TI 52 GLU cc_start: 0.9089 (tt0) cc_final: 0.8812 (tt0) REVERT: TI 58 ASP cc_start: 0.8801 (t0) cc_final: 0.8402 (t0) REVERT: TI 59 ASP cc_start: 0.9163 (m-30) cc_final: 0.8631 (t0) REVERT: TI 83 GLN cc_start: 0.9071 (mt0) cc_final: 0.8560 (tp40) REVERT: TI 92 THR cc_start: 0.9577 (m) cc_final: 0.9135 (p) REVERT: TI 112 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8721 (mt-10) REVERT: TA 22 SER cc_start: 0.9014 (t) cc_final: 0.8728 (m) REVERT: TA 24 SER cc_start: 0.9009 (m) cc_final: 0.8758 (t) REVERT: TA 89 THR cc_start: 0.9206 (m) cc_final: 0.8737 (p) REVERT: TA 189 ASP cc_start: 0.9140 (t70) cc_final: 0.8790 (t0) REVERT: TB 24 SER cc_start: 0.9146 (m) cc_final: 0.8828 (t) REVERT: TB 54 THR cc_start: 0.9457 (m) cc_final: 0.9175 (p) REVERT: TB 89 THR cc_start: 0.9141 (m) cc_final: 0.8736 (p) REVERT: TB 189 ASP cc_start: 0.9085 (t0) cc_final: 0.8751 (t70) REVERT: TB 319 MET cc_start: 0.9438 (tmm) cc_final: 0.9169 (tmm) outliers start: 47 outliers final: 24 residues processed: 373 average time/residue: 0.5178 time to fit residues: 216.1334 Evaluate side-chains 362 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TC residue 315 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 188 ILE Chi-restraints excluded: chain TB residue 315 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 31 GLN TE 42 ASN TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.070378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.059504 restraints weight = 24496.162| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 2.27 r_work: 0.2408 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14760 Z= 0.143 Angle : 0.490 5.822 20094 Z= 0.270 Chirality : 0.045 0.147 2319 Planarity : 0.003 0.035 2685 Dihedral : 5.914 53.490 2067 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.70 % Allowed : 15.09 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1884 helix: 2.18 (0.32), residues: 264 sheet: 0.10 (0.20), residues: 654 loop : -0.72 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGTI 111 TYR 0.025 0.002 TYRTB 290 PHE 0.016 0.001 PHETB 354 TRP 0.006 0.001 TRPTC 65 HIS 0.003 0.001 HISTB 304 Details of bonding type rmsd covalent geometry : bond 0.00318 (14754) covalent geometry : angle 0.48990 (20094) hydrogen bonds : bond 0.03313 ( 402) hydrogen bonds : angle 4.68460 ( 1110) metal coordination : bond 0.00184 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 338 time to evaluate : 0.588 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8577 (t0) cc_final: 0.8146 (t0) REVERT: TC 22 SER cc_start: 0.9173 (t) cc_final: 0.8678 (m) REVERT: TC 89 THR cc_start: 0.9128 (m) cc_final: 0.8680 (p) REVERT: TC 139 THR cc_start: 0.9622 (OUTLIER) cc_final: 0.9156 (t) REVERT: TD 58 ASP cc_start: 0.8733 (t70) cc_final: 0.8200 (t70) REVERT: TD 63 VAL cc_start: 0.9317 (t) cc_final: 0.8863 (m) REVERT: TD 83 GLN cc_start: 0.8986 (mt0) cc_final: 0.8543 (mt0) REVERT: TD 85 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8531 (mt-10) REVERT: TD 111 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8636 (mtt90) REVERT: TE 9 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8624 (tp40) REVERT: TE 24 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8506 (mt-10) REVERT: TE 58 ASP cc_start: 0.8893 (t0) cc_final: 0.8569 (t0) REVERT: TE 92 THR cc_start: 0.9467 (m) cc_final: 0.8970 (p) REVERT: TF 58 ASP cc_start: 0.8574 (t0) cc_final: 0.7874 (t0) REVERT: TF 59 ASP cc_start: 0.9176 (m-30) cc_final: 0.8624 (t70) REVERT: TF 61 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8558 (mt-10) REVERT: TF 83 GLN cc_start: 0.9027 (mt0) cc_final: 0.8580 (mt0) REVERT: TF 85 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8411 (mt-10) REVERT: TF 112 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8431 (mt-10) REVERT: TG 39 GLU cc_start: 0.8927 (tt0) cc_final: 0.8501 (tt0) REVERT: TG 52 GLU cc_start: 0.9013 (tt0) cc_final: 0.8779 (tt0) REVERT: TG 58 ASP cc_start: 0.8869 (t70) cc_final: 0.8379 (t70) REVERT: TG 83 GLN cc_start: 0.9006 (tt0) cc_final: 0.8683 (tt0) REVERT: TG 92 THR cc_start: 0.9601 (m) cc_final: 0.9096 (p) REVERT: TH 58 ASP cc_start: 0.8688 (t0) cc_final: 0.8232 (t70) REVERT: TH 59 ASP cc_start: 0.9240 (m-30) cc_final: 0.8790 (t0) REVERT: TH 83 GLN cc_start: 0.8935 (mt0) cc_final: 0.8391 (mt0) REVERT: TH 92 THR cc_start: 0.9582 (m) cc_final: 0.9114 (p) REVERT: TH 112 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: TI 24 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8475 (mt-10) REVERT: TI 29 ASP cc_start: 0.8917 (t0) cc_final: 0.8713 (t0) REVERT: TI 58 ASP cc_start: 0.8791 (t0) cc_final: 0.8347 (t0) REVERT: TI 59 ASP cc_start: 0.9168 (m-30) cc_final: 0.8639 (t0) REVERT: TI 83 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8607 (tp40) REVERT: TI 92 THR cc_start: 0.9564 (m) cc_final: 0.9108 (p) REVERT: TI 112 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8688 (mt-10) REVERT: TA 22 SER cc_start: 0.9008 (t) cc_final: 0.8712 (m) REVERT: TA 24 SER cc_start: 0.9001 (m) cc_final: 0.8755 (t) REVERT: TA 89 THR cc_start: 0.9182 (m) cc_final: 0.8725 (p) REVERT: TA 189 ASP cc_start: 0.9076 (t70) cc_final: 0.8708 (t0) REVERT: TB 24 SER cc_start: 0.9137 (m) cc_final: 0.8802 (t) REVERT: TB 54 THR cc_start: 0.9477 (m) cc_final: 0.9194 (p) REVERT: TB 89 THR cc_start: 0.9133 (m) cc_final: 0.8735 (p) REVERT: TB 189 ASP cc_start: 0.9087 (t0) cc_final: 0.8746 (t70) REVERT: TB 319 MET cc_start: 0.9438 (tmm) cc_final: 0.9176 (tmm) outliers start: 43 outliers final: 26 residues processed: 360 average time/residue: 0.5098 time to fit residues: 205.4149 Evaluate side-chains 354 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 315 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 55 THR Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 27 LEU Chi-restraints excluded: chain TE residue 55 THR Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TF residue 80 GLN Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 90 optimal weight: 0.0570 chunk 110 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN TD 42 ASN TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN ** TA 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.067203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.056115 restraints weight = 24939.752| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 2.30 r_work: 0.2357 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2238 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14760 Z= 0.258 Angle : 0.538 7.430 20094 Z= 0.294 Chirality : 0.046 0.162 2319 Planarity : 0.004 0.041 2685 Dihedral : 6.058 53.507 2067 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.89 % Allowed : 15.47 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.19), residues: 1884 helix: 2.18 (0.32), residues: 261 sheet: 0.04 (0.21), residues: 636 loop : -0.68 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGTA 133 TYR 0.026 0.002 TYRTC 290 PHE 0.019 0.002 PHETB 354 TRP 0.007 0.001 TRPTC 65 HIS 0.005 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00576 (14754) covalent geometry : angle 0.53821 (20094) hydrogen bonds : bond 0.03600 ( 402) hydrogen bonds : angle 4.81660 ( 1110) metal coordination : bond 0.00396 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 0.589 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8552 (t0) cc_final: 0.8108 (t0) REVERT: TC 89 THR cc_start: 0.9125 (m) cc_final: 0.8690 (p) REVERT: TC 139 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9148 (t) REVERT: TD 58 ASP cc_start: 0.8740 (t70) cc_final: 0.8204 (t70) REVERT: TD 63 VAL cc_start: 0.9229 (t) cc_final: 0.8747 (m) REVERT: TD 83 GLN cc_start: 0.9026 (mt0) cc_final: 0.8516 (mt0) REVERT: TD 85 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8552 (mt-10) REVERT: TE 9 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8584 (tp40) REVERT: TE 24 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8536 (mt-10) REVERT: TE 58 ASP cc_start: 0.8842 (t0) cc_final: 0.8507 (t0) REVERT: TE 92 THR cc_start: 0.9440 (m) cc_final: 0.8974 (p) REVERT: TF 29 ASP cc_start: 0.9079 (t0) cc_final: 0.8712 (t0) REVERT: TF 58 ASP cc_start: 0.8528 (t0) cc_final: 0.7792 (t0) REVERT: TF 59 ASP cc_start: 0.9121 (m-30) cc_final: 0.8638 (t70) REVERT: TF 61 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8543 (mt-10) REVERT: TF 65 ASP cc_start: 0.8963 (t0) cc_final: 0.8757 (t0) REVERT: TF 83 GLN cc_start: 0.9121 (mt0) cc_final: 0.8499 (tt0) REVERT: TF 85 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8401 (mt-10) REVERT: TF 112 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8526 (mt-10) REVERT: TG 39 GLU cc_start: 0.8979 (tt0) cc_final: 0.8610 (tt0) REVERT: TG 52 GLU cc_start: 0.9008 (tt0) cc_final: 0.8740 (tt0) REVERT: TG 58 ASP cc_start: 0.8816 (t70) cc_final: 0.8351 (t70) REVERT: TG 92 THR cc_start: 0.9621 (m) cc_final: 0.9104 (p) REVERT: TH 52 GLU cc_start: 0.8929 (tt0) cc_final: 0.8562 (tt0) REVERT: TH 58 ASP cc_start: 0.8687 (t0) cc_final: 0.8226 (t0) REVERT: TH 59 ASP cc_start: 0.9228 (m-30) cc_final: 0.8788 (t0) REVERT: TH 83 GLN cc_start: 0.8934 (mt0) cc_final: 0.8459 (mt0) REVERT: TH 92 THR cc_start: 0.9570 (m) cc_final: 0.9122 (p) REVERT: TH 112 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: TI 24 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8477 (mt-10) REVERT: TI 29 ASP cc_start: 0.8915 (t0) cc_final: 0.8710 (t0) REVERT: TI 58 ASP cc_start: 0.8689 (t0) cc_final: 0.8242 (t0) REVERT: TI 59 ASP cc_start: 0.9161 (m-30) cc_final: 0.8636 (t0) REVERT: TI 83 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: TI 92 THR cc_start: 0.9560 (m) cc_final: 0.9118 (p) REVERT: TI 112 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8692 (mt-10) REVERT: TA 22 SER cc_start: 0.8998 (t) cc_final: 0.8689 (m) REVERT: TA 24 SER cc_start: 0.8993 (m) cc_final: 0.8722 (t) REVERT: TA 54 THR cc_start: 0.9532 (m) cc_final: 0.9175 (p) REVERT: TA 89 THR cc_start: 0.9179 (m) cc_final: 0.8698 (p) REVERT: TA 133 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7835 (ttp80) REVERT: TA 189 ASP cc_start: 0.9162 (t70) cc_final: 0.8703 (t70) REVERT: TB 24 SER cc_start: 0.9119 (m) cc_final: 0.8774 (t) REVERT: TB 54 THR cc_start: 0.9446 (m) cc_final: 0.9152 (p) REVERT: TB 89 THR cc_start: 0.9126 (m) cc_final: 0.8665 (p) REVERT: TB 164 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9001 (tt0) REVERT: TB 189 ASP cc_start: 0.9028 (t0) cc_final: 0.8709 (t0) REVERT: TB 319 MET cc_start: 0.9395 (tmm) cc_final: 0.9098 (tmm) outliers start: 46 outliers final: 31 residues processed: 372 average time/residue: 0.5164 time to fit residues: 214.2243 Evaluate side-chains 380 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TC residue 315 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 55 THR Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 55 THR Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 7 ASN Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 133 ARG Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 164 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN TH 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.069276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.058049 restraints weight = 24912.747| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.36 r_work: 0.2380 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2260 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14760 Z= 0.160 Angle : 0.498 5.806 20094 Z= 0.274 Chirality : 0.045 0.144 2319 Planarity : 0.003 0.036 2685 Dihedral : 5.916 53.136 2067 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.70 % Allowed : 15.85 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.19), residues: 1884 helix: 2.17 (0.32), residues: 264 sheet: 0.03 (0.20), residues: 648 loop : -0.76 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGTA 133 TYR 0.024 0.002 TYRTB 290 PHE 0.017 0.001 PHETB 354 TRP 0.006 0.001 TRPTC 65 HIS 0.003 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00357 (14754) covalent geometry : angle 0.49838 (20094) hydrogen bonds : bond 0.03303 ( 402) hydrogen bonds : angle 4.73840 ( 1110) metal coordination : bond 0.00217 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 337 time to evaluate : 0.641 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8608 (t0) cc_final: 0.8174 (t0) REVERT: TC 22 SER cc_start: 0.9271 (t) cc_final: 0.8769 (m) REVERT: TC 89 THR cc_start: 0.9142 (m) cc_final: 0.8685 (p) REVERT: TC 139 THR cc_start: 0.9610 (OUTLIER) cc_final: 0.9150 (t) REVERT: TD 24 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8789 (pm20) REVERT: TD 58 ASP cc_start: 0.8845 (t70) cc_final: 0.8557 (t70) REVERT: TD 83 GLN cc_start: 0.9021 (mt0) cc_final: 0.8543 (mt0) REVERT: TD 85 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8508 (mt-10) REVERT: TE 9 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8640 (tp40) REVERT: TE 24 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8514 (mt-10) REVERT: TE 58 ASP cc_start: 0.8916 (t0) cc_final: 0.8561 (t0) REVERT: TE 92 THR cc_start: 0.9485 (m) cc_final: 0.9025 (p) REVERT: TF 58 ASP cc_start: 0.8578 (t0) cc_final: 0.7869 (t0) REVERT: TF 59 ASP cc_start: 0.9149 (m-30) cc_final: 0.8664 (t70) REVERT: TF 61 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8559 (mt-10) REVERT: TF 83 GLN cc_start: 0.9074 (mt0) cc_final: 0.8584 (tt0) REVERT: TF 112 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8494 (mt-10) REVERT: TG 24 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8614 (mt-10) REVERT: TG 39 GLU cc_start: 0.8943 (tt0) cc_final: 0.8538 (tt0) REVERT: TG 58 ASP cc_start: 0.8877 (t70) cc_final: 0.8383 (t70) REVERT: TG 92 THR cc_start: 0.9628 (m) cc_final: 0.9113 (p) REVERT: TH 58 ASP cc_start: 0.8721 (t0) cc_final: 0.8257 (t0) REVERT: TH 59 ASP cc_start: 0.9238 (m-30) cc_final: 0.8805 (t0) REVERT: TH 83 GLN cc_start: 0.8925 (mt0) cc_final: 0.8421 (mt0) REVERT: TH 85 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8847 (mt-10) REVERT: TH 92 THR cc_start: 0.9574 (m) cc_final: 0.9104 (p) REVERT: TH 112 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8663 (tt0) REVERT: TI 24 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8466 (mt-10) REVERT: TI 29 ASP cc_start: 0.8931 (t0) cc_final: 0.8720 (t0) REVERT: TI 58 ASP cc_start: 0.8773 (t0) cc_final: 0.8320 (t0) REVERT: TI 59 ASP cc_start: 0.9173 (m-30) cc_final: 0.8658 (t0) REVERT: TI 83 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: TI 92 THR cc_start: 0.9581 (m) cc_final: 0.9136 (p) REVERT: TI 112 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8688 (mt-10) REVERT: TA 22 SER cc_start: 0.9032 (t) cc_final: 0.8718 (m) REVERT: TA 24 SER cc_start: 0.9029 (m) cc_final: 0.8780 (t) REVERT: TA 89 THR cc_start: 0.9219 (m) cc_final: 0.8753 (p) REVERT: TA 189 ASP cc_start: 0.9158 (t70) cc_final: 0.8755 (t70) REVERT: TB 24 SER cc_start: 0.9155 (m) cc_final: 0.8828 (t) REVERT: TB 54 THR cc_start: 0.9454 (m) cc_final: 0.9158 (p) REVERT: TB 89 THR cc_start: 0.9153 (m) cc_final: 0.8725 (p) REVERT: TB 164 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9013 (tt0) REVERT: TB 189 ASP cc_start: 0.9061 (t0) cc_final: 0.8740 (t0) REVERT: TB 319 MET cc_start: 0.9445 (tmm) cc_final: 0.9166 (tmm) outliers start: 43 outliers final: 28 residues processed: 363 average time/residue: 0.5098 time to fit residues: 207.2209 Evaluate side-chains 360 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TC residue 315 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 55 THR Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 38 ILE Chi-restraints excluded: chain TE residue 55 THR Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 116 optimal weight: 0.4980 chunk 134 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 42 ASN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.069418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.058467 restraints weight = 24789.452| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 2.28 r_work: 0.2394 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14760 Z= 0.183 Angle : 0.515 6.927 20094 Z= 0.282 Chirality : 0.045 0.146 2319 Planarity : 0.003 0.036 2685 Dihedral : 5.918 52.916 2067 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 16.60 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.19), residues: 1884 helix: 2.19 (0.32), residues: 261 sheet: 0.11 (0.20), residues: 642 loop : -0.81 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGTI 95 TYR 0.025 0.002 TYRTC 290 PHE 0.017 0.001 PHETB 354 TRP 0.006 0.001 TRPTA 65 HIS 0.004 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00414 (14754) covalent geometry : angle 0.51475 (20094) hydrogen bonds : bond 0.03315 ( 402) hydrogen bonds : angle 4.75889 ( 1110) metal coordination : bond 0.00255 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 0.508 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8563 (t0) cc_final: 0.8126 (t0) REVERT: TC 89 THR cc_start: 0.9146 (m) cc_final: 0.8684 (p) REVERT: TC 139 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9146 (t) REVERT: TD 58 ASP cc_start: 0.8842 (t70) cc_final: 0.8499 (t70) REVERT: TD 83 GLN cc_start: 0.9016 (mt0) cc_final: 0.8508 (mt0) REVERT: TD 85 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8436 (mt-10) REVERT: TE 9 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8685 (tp40) REVERT: TE 24 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8496 (mt-10) REVERT: TE 58 ASP cc_start: 0.8906 (t0) cc_final: 0.8541 (t0) REVERT: TE 92 THR cc_start: 0.9472 (m) cc_final: 0.8977 (p) REVERT: TF 58 ASP cc_start: 0.8553 (t0) cc_final: 0.7832 (t0) REVERT: TF 59 ASP cc_start: 0.9137 (m-30) cc_final: 0.8650 (t70) REVERT: TF 61 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8530 (mt-10) REVERT: TF 83 GLN cc_start: 0.8876 (mt0) cc_final: 0.8358 (tt0) REVERT: TF 112 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8520 (mt-10) REVERT: TG 24 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8594 (mt-10) REVERT: TG 39 GLU cc_start: 0.8960 (tt0) cc_final: 0.8549 (tt0) REVERT: TG 58 ASP cc_start: 0.8866 (t70) cc_final: 0.8378 (t70) REVERT: TG 92 THR cc_start: 0.9621 (m) cc_final: 0.9104 (p) REVERT: TH 58 ASP cc_start: 0.8721 (t0) cc_final: 0.8248 (t0) REVERT: TH 59 ASP cc_start: 0.9224 (m-30) cc_final: 0.8797 (t0) REVERT: TH 83 GLN cc_start: 0.8928 (mt0) cc_final: 0.8409 (mt0) REVERT: TH 85 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8835 (mt-10) REVERT: TH 92 THR cc_start: 0.9570 (m) cc_final: 0.9096 (p) REVERT: TH 112 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: TI 24 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8474 (mt-10) REVERT: TI 58 ASP cc_start: 0.8758 (t0) cc_final: 0.8299 (t0) REVERT: TI 59 ASP cc_start: 0.9176 (m-30) cc_final: 0.8653 (t0) REVERT: TI 83 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: TI 92 THR cc_start: 0.9571 (m) cc_final: 0.9117 (p) REVERT: TI 112 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8683 (mt-10) REVERT: TA 22 SER cc_start: 0.9011 (t) cc_final: 0.8677 (m) REVERT: TA 24 SER cc_start: 0.9009 (m) cc_final: 0.8746 (t) REVERT: TA 89 THR cc_start: 0.9209 (m) cc_final: 0.8761 (p) REVERT: TA 189 ASP cc_start: 0.9152 (t0) cc_final: 0.8720 (t70) REVERT: TB 24 SER cc_start: 0.9137 (m) cc_final: 0.8805 (t) REVERT: TB 54 THR cc_start: 0.9447 (m) cc_final: 0.9142 (p) REVERT: TB 89 THR cc_start: 0.9139 (m) cc_final: 0.8700 (p) REVERT: TB 189 ASP cc_start: 0.9044 (t0) cc_final: 0.8744 (t0) REVERT: TB 319 MET cc_start: 0.9425 (tmm) cc_final: 0.9135 (tmm) outliers start: 35 outliers final: 27 residues processed: 345 average time/residue: 0.4737 time to fit residues: 183.5171 Evaluate side-chains 347 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 55 THR Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 38 ILE Chi-restraints excluded: chain TE residue 55 THR Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 54 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 138 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.070000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.059034 restraints weight = 24621.257| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 2.27 r_work: 0.2397 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14760 Z= 0.154 Angle : 0.506 6.601 20094 Z= 0.277 Chirality : 0.045 0.144 2319 Planarity : 0.003 0.035 2685 Dihedral : 5.866 52.513 2067 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 16.86 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.19), residues: 1884 helix: 2.27 (0.32), residues: 261 sheet: 0.14 (0.20), residues: 636 loop : -0.86 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGTI 95 TYR 0.025 0.002 TYRTB 290 PHE 0.016 0.001 PHETB 354 TRP 0.006 0.001 TRPTA 65 HIS 0.003 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00345 (14754) covalent geometry : angle 0.50609 (20094) hydrogen bonds : bond 0.03185 ( 402) hydrogen bonds : angle 4.71302 ( 1110) metal coordination : bond 0.00207 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 0.582 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8562 (t0) cc_final: 0.8119 (t0) REVERT: TC 89 THR cc_start: 0.9097 (m) cc_final: 0.8676 (p) REVERT: TC 139 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9123 (t) REVERT: TD 58 ASP cc_start: 0.8837 (t70) cc_final: 0.8537 (t70) REVERT: TD 83 GLN cc_start: 0.9003 (mt0) cc_final: 0.8512 (mt0) REVERT: TD 85 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8445 (mt-10) REVERT: TD 92 THR cc_start: 0.9426 (m) cc_final: 0.8934 (p) REVERT: TE 9 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8670 (tp40) REVERT: TE 24 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8480 (mt-10) REVERT: TE 58 ASP cc_start: 0.8878 (t0) cc_final: 0.8499 (t0) REVERT: TE 92 THR cc_start: 0.9469 (m) cc_final: 0.8974 (p) REVERT: TF 58 ASP cc_start: 0.8536 (t0) cc_final: 0.7805 (t0) REVERT: TF 59 ASP cc_start: 0.9130 (m-30) cc_final: 0.8762 (t70) REVERT: TF 61 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8543 (mt-10) REVERT: TF 83 GLN cc_start: 0.8945 (mt0) cc_final: 0.8154 (tt0) REVERT: TF 85 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8596 (mt-10) REVERT: TF 112 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8479 (mt-10) REVERT: TG 24 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8597 (mt-10) REVERT: TG 39 GLU cc_start: 0.8928 (tt0) cc_final: 0.8477 (tt0) REVERT: TG 58 ASP cc_start: 0.8865 (t70) cc_final: 0.8392 (t70) REVERT: TG 83 GLN cc_start: 0.9031 (tt0) cc_final: 0.8699 (tt0) REVERT: TG 92 THR cc_start: 0.9608 (m) cc_final: 0.9081 (p) REVERT: TH 58 ASP cc_start: 0.8716 (t0) cc_final: 0.8230 (t0) REVERT: TH 59 ASP cc_start: 0.9265 (m-30) cc_final: 0.8757 (t0) REVERT: TH 83 GLN cc_start: 0.8888 (mt0) cc_final: 0.8373 (mt0) REVERT: TH 85 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8917 (mt-10) REVERT: TH 92 THR cc_start: 0.9561 (m) cc_final: 0.9074 (p) REVERT: TH 112 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (tt0) REVERT: TI 24 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8508 (mt-10) REVERT: TI 58 ASP cc_start: 0.8722 (t0) cc_final: 0.8250 (t0) REVERT: TI 59 ASP cc_start: 0.9204 (m-30) cc_final: 0.8707 (t0) REVERT: TI 83 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: TI 92 THR cc_start: 0.9565 (m) cc_final: 0.9107 (p) REVERT: TI 112 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8646 (mt-10) REVERT: TA 22 SER cc_start: 0.9004 (t) cc_final: 0.8664 (m) REVERT: TA 24 SER cc_start: 0.9004 (m) cc_final: 0.8744 (t) REVERT: TA 89 THR cc_start: 0.9188 (m) cc_final: 0.8745 (p) REVERT: TA 189 ASP cc_start: 0.9147 (t0) cc_final: 0.8711 (t70) REVERT: TB 24 SER cc_start: 0.9125 (m) cc_final: 0.8789 (t) REVERT: TB 54 THR cc_start: 0.9429 (m) cc_final: 0.9114 (p) REVERT: TB 89 THR cc_start: 0.9137 (m) cc_final: 0.8703 (p) REVERT: TB 164 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8982 (tt0) REVERT: TB 189 ASP cc_start: 0.9096 (t0) cc_final: 0.8737 (t0) REVERT: TB 319 MET cc_start: 0.9416 (tmm) cc_final: 0.9121 (tmm) outliers start: 32 outliers final: 26 residues processed: 348 average time/residue: 0.4873 time to fit residues: 190.0808 Evaluate side-chains 351 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain TC residue 194 ASP Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 40 ILE Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 55 THR Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TE residue 38 ILE Chi-restraints excluded: chain TE residue 55 THR Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TF residue 80 GLN Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 19 SER Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN TD 42 ASN ** TE 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 31 GLN TE 42 ASN TF 31 GLN TF 80 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 80 GLN TI 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.069010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.057864 restraints weight = 24841.466| |-----------------------------------------------------------------------------| r_work (start): 0.2517 rms_B_bonded: 2.33 r_work: 0.2387 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14760 Z= 0.165 Angle : 0.512 5.744 20094 Z= 0.280 Chirality : 0.045 0.145 2319 Planarity : 0.003 0.035 2685 Dihedral : 5.865 52.424 2067 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.26 % Allowed : 16.86 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.19), residues: 1884 helix: 2.27 (0.32), residues: 261 sheet: 0.15 (0.20), residues: 636 loop : -0.87 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGTI 95 TYR 0.025 0.002 TYRTC 290 PHE 0.016 0.001 PHETB 354 TRP 0.005 0.001 TRPTC 65 HIS 0.003 0.001 HISTA 304 Details of bonding type rmsd covalent geometry : bond 0.00370 (14754) covalent geometry : angle 0.51196 (20094) hydrogen bonds : bond 0.03208 ( 402) hydrogen bonds : angle 4.72044 ( 1110) metal coordination : bond 0.00224 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.62 seconds wall clock time: 105 minutes 44.83 seconds (6344.83 seconds total)