Starting phenix.real_space_refine on Fri Jun 13 02:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpg_18550/06_2025/8qpg_18550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpg_18550/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpg_18550/06_2025/8qpg_18550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpg_18550/06_2025/8qpg_18550.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpg_18550/06_2025/8qpg_18550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpg_18550/06_2025/8qpg_18550.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.29, per 1000 atoms: 1.19 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: 5.76 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNTA 501 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 270 " pdb="ZN ZNTA 501 " - pdb=" NE2 HISTA 266 " pdb=" ZNTB 501 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 270 " pdb="ZN ZNTB 501 " - pdb=" NE2 HISTB 266 " pdb=" ZNTC 501 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 270 " pdb="ZN ZNTC 501 " - pdb=" NE2 HISTC 266 " 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: 2.36 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: 7.71 Time building geometry restraints manager: 6.51 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: 0.08 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: 0.010 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 61.000 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:31.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (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 TRP 0.057 0.018 TRPTB 156 HIS 0.019 0.005 HISTA 214 PHE 0.049 0.010 PHETA 354 TYR 0.087 0.013 TYRTA 305 ARG 0.027 0.003 ARGTA 118 Details of bonding type rmsd hydrogen bonds : bond 0.13387 ( 402) hydrogen bonds : angle 6.79728 ( 1110) metal coordination : bond 0.40976 ( 6) covalent geometry : bond 0.00825 (14754) covalent geometry : angle 1.49983 (20094) *********************** 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 : 2.299 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: 1.1219 time to fit residues: 672.2734 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 : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 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 324 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.070793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.060011 restraints weight = 24336.677| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 2.25 r_work: 0.2409 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2289 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14760 Z= 0.156 Angle : 0.546 6.114 20094 Z= 0.308 Chirality : 0.046 0.143 2319 Planarity : 0.003 0.037 2685 Dihedral : 6.660 55.727 2067 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1884 helix: 1.63 (0.31), residues: 261 sheet: 0.56 (0.20), residues: 669 loop : -0.66 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPTC 65 HIS 0.004 0.001 HISTB 266 PHE 0.019 0.002 PHETA 354 TYR 0.027 0.002 TYRTB 290 ARG 0.009 0.001 ARGTB 52 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 402) hydrogen bonds : angle 5.10646 ( 1110) metal coordination : bond 0.00809 ( 6) covalent geometry : bond 0.00342 (14754) covalent geometry : angle 0.54557 (20094) *********************** 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 448 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 406 time to evaluate : 1.564 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8746 (t0) cc_final: 0.8255 (t0) REVERT: TC 22 SER cc_start: 0.9151 (t) cc_final: 0.8718 (m) REVERT: TC 89 THR cc_start: 0.9094 (m) cc_final: 0.8610 (p) REVERT: TC 189 ASP cc_start: 0.8825 (t70) cc_final: 0.8617 (t70) REVERT: TC 199 ASP cc_start: 0.8917 (t0) cc_final: 0.8695 (t0) REVERT: TC 400 ASP cc_start: 0.9294 (t70) cc_final: 0.9080 (t0) REVERT: TD 29 ASP cc_start: 0.8803 (t0) cc_final: 0.8588 (t0) REVERT: TD 55 THR cc_start: 0.9240 (m) cc_final: 0.8973 (t) REVERT: TD 58 ASP cc_start: 0.8621 (t70) cc_final: 0.8256 (t0) REVERT: TD 63 VAL cc_start: 0.9290 (t) cc_final: 0.8875 (m) REVERT: TD 65 ASP cc_start: 0.8971 (t0) cc_final: 0.8767 (t0) REVERT: TD 71 ASP cc_start: 0.9049 (t0) cc_final: 0.8756 (t0) REVERT: TD 83 GLN cc_start: 0.9009 (mt0) cc_final: 0.8357 (mt0) REVERT: TD 85 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8766 (mt-10) REVERT: TD 92 THR cc_start: 0.9511 (m) cc_final: 0.8884 (p) REVERT: TE 24 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8443 (mt-10) REVERT: TE 58 ASP cc_start: 0.8878 (t0) cc_final: 0.8637 (t0) REVERT: TE 59 ASP cc_start: 0.9287 (m-30) cc_final: 0.8615 (t0) REVERT: TE 64 GLU cc_start: 0.8639 (tt0) cc_final: 0.8161 (tm-30) REVERT: TE 92 THR cc_start: 0.9534 (m) cc_final: 0.9004 (p) REVERT: TF 29 ASP cc_start: 0.8990 (t0) cc_final: 0.8727 (t0) REVERT: TF 39 GLU cc_start: 0.8971 (tt0) cc_final: 0.8443 (tt0) REVERT: TF 58 ASP cc_start: 0.8547 (t0) cc_final: 0.8015 (t0) REVERT: TF 59 ASP cc_start: 0.9230 (m-30) cc_final: 0.8591 (t70) REVERT: TF 61 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8620 (mt-10) REVERT: TF 63 VAL cc_start: 0.9301 (t) cc_final: 0.8974 (m) REVERT: TF 83 GLN cc_start: 0.9068 (mt0) cc_final: 0.8480 (tt0) REVERT: TF 92 THR cc_start: 0.9556 (m) cc_final: 0.9078 (p) REVERT: TF 112 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8536 (mt-10) REVERT: TG 39 GLU cc_start: 0.8920 (tt0) cc_final: 0.8522 (tt0) REVERT: TG 58 ASP cc_start: 0.8786 (t70) cc_final: 0.8318 (t0) REVERT: TG 63 VAL cc_start: 0.9007 (t) cc_final: 0.8538 (m) REVERT: TG 83 GLN cc_start: 0.8851 (tt0) cc_final: 0.8472 (tt0) REVERT: TG 92 THR cc_start: 0.9595 (m) cc_final: 0.9143 (p) REVERT: TG 112 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8729 (mt-10) REVERT: TH 5 ILE cc_start: 0.9330 (mt) cc_final: 0.9130 (mp) REVERT: TH 58 ASP cc_start: 0.8613 (t0) cc_final: 0.8353 (t0) REVERT: TH 59 ASP cc_start: 0.9262 (m-30) cc_final: 0.8682 (t0) REVERT: TH 83 GLN cc_start: 0.8948 (mt0) cc_final: 0.8440 (tt0) REVERT: TH 92 THR cc_start: 0.9528 (m) cc_final: 0.9108 (p) REVERT: TI 29 ASP cc_start: 0.8824 (t0) cc_final: 0.8522 (t0) REVERT: TI 58 ASP cc_start: 0.8731 (t0) cc_final: 0.8515 (t0) REVERT: TI 59 ASP cc_start: 0.9125 (m-30) cc_final: 0.8647 (t0) REVERT: TI 63 VAL cc_start: 0.9064 (t) cc_final: 0.8585 (m) REVERT: TI 83 GLN cc_start: 0.8994 (mt0) cc_final: 0.8627 (tt0) REVERT: TI 92 THR cc_start: 0.9591 (m) cc_final: 0.9099 (p) REVERT: TI 112 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8763 (mt-10) REVERT: TA 22 SER cc_start: 0.9116 (t) cc_final: 0.8782 (m) REVERT: TA 24 SER cc_start: 0.9003 (m) cc_final: 0.8759 (t) REVERT: TA 38 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8952 (mpp80) REVERT: TA 69 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8837 (tp) REVERT: TA 89 THR cc_start: 0.9120 (m) cc_final: 0.8700 (p) REVERT: TA 116 LEU cc_start: 0.9055 (tt) cc_final: 0.8755 (tt) REVERT: TB 7 ASP cc_start: 0.8847 (t0) cc_final: 0.8641 (t0) REVERT: TB 19 SER cc_start: 0.9158 (t) cc_final: 0.8844 (p) REVERT: TB 24 SER cc_start: 0.9108 (m) cc_final: 0.8801 (t) REVERT: TB 89 THR cc_start: 0.9097 (m) cc_final: 0.8692 (p) REVERT: TB 189 ASP cc_start: 0.9017 (t0) cc_final: 0.8795 (t0) REVERT: TB 315 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8805 (mt-10) REVERT: TB 319 MET cc_start: 0.9414 (tmm) cc_final: 0.9116 (tmm) REVERT: TB 333 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8410 (mt-10) outliers start: 42 outliers final: 12 residues processed: 425 average time/residue: 0.9617 time to fit residues: 462.2228 Evaluate side-chains 358 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 344 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 155 optimal weight: 0.0070 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 214 HIS ** 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 TF 80 GLN TH 31 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN TA 68 ASN TB 260 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.069480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.058667 restraints weight = 24417.354| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 2.25 r_work: 0.2394 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2380 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= 0.194 Angle : 0.524 7.347 20094 Z= 0.292 Chirality : 0.045 0.151 2319 Planarity : 0.003 0.036 2685 Dihedral : 6.266 55.164 2067 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.77 % Allowed : 11.51 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1884 helix: 1.88 (0.32), residues: 264 sheet: 0.33 (0.20), residues: 675 loop : -0.56 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPTC 65 HIS 0.005 0.001 HISTB 304 PHE 0.020 0.002 PHETA 354 TYR 0.026 0.002 TYRTB 290 ARG 0.006 0.001 ARGTA 133 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 402) hydrogen bonds : angle 4.90107 ( 1110) metal coordination : bond 0.00385 ( 6) covalent geometry : bond 0.00433 (14754) covalent geometry : angle 0.52426 (20094) *********************** 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 409 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 1.557 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8581 (t0) cc_final: 0.8107 (t0) REVERT: TC 22 SER cc_start: 0.9190 (t) cc_final: 0.8726 (m) REVERT: TC 89 THR cc_start: 0.9136 (m) cc_final: 0.8706 (p) REVERT: TC 189 ASP cc_start: 0.8905 (t70) cc_final: 0.8639 (t70) REVERT: TC 199 ASP cc_start: 0.8939 (t0) cc_final: 0.8693 (t0) REVERT: TC 217 ASP cc_start: 0.9257 (m-30) cc_final: 0.8738 (m-30) REVERT: TC 400 ASP cc_start: 0.9261 (t70) cc_final: 0.9043 (t0) REVERT: TD 58 ASP cc_start: 0.8638 (t70) cc_final: 0.8168 (t0) REVERT: TD 63 VAL cc_start: 0.9290 (t) cc_final: 0.8808 (m) REVERT: TD 83 GLN cc_start: 0.9040 (mt0) cc_final: 0.8646 (mt0) REVERT: TD 85 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8720 (mt-10) REVERT: TD 92 THR cc_start: 0.9516 (m) cc_final: 0.8980 (p) REVERT: TE 24 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8542 (mt-10) REVERT: TE 58 ASP cc_start: 0.8927 (t0) cc_final: 0.8545 (t0) REVERT: TE 59 ASP cc_start: 0.9297 (m-30) cc_final: 0.8791 (t0) REVERT: TE 83 GLN cc_start: 0.9184 (tt0) cc_final: 0.8611 (tp40) REVERT: TE 92 THR cc_start: 0.9514 (m) cc_final: 0.9030 (p) REVERT: TF 29 ASP cc_start: 0.9040 (t0) cc_final: 0.8779 (t0) REVERT: TF 39 GLU cc_start: 0.9043 (tt0) cc_final: 0.8647 (tt0) REVERT: TF 58 ASP cc_start: 0.8612 (t0) cc_final: 0.8002 (t0) REVERT: TF 59 ASP cc_start: 0.9178 (m-30) cc_final: 0.8602 (t70) REVERT: TF 61 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8595 (mt-10) REVERT: TF 83 GLN cc_start: 0.9091 (mt0) cc_final: 0.8611 (tt0) REVERT: TF 112 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8520 (mt-10) REVERT: TG 39 GLU cc_start: 0.8996 (tt0) cc_final: 0.8582 (tt0) REVERT: TG 58 ASP cc_start: 0.8855 (t70) cc_final: 0.8305 (t0) REVERT: TG 83 GLN cc_start: 0.9041 (tt0) cc_final: 0.8640 (tt0) REVERT: TG 92 THR cc_start: 0.9607 (m) cc_final: 0.9121 (p) REVERT: TH 58 ASP cc_start: 0.8676 (t0) cc_final: 0.8331 (t0) REVERT: TH 59 ASP cc_start: 0.9264 (m-30) cc_final: 0.8790 (t0) REVERT: TH 83 GLN cc_start: 0.8958 (mt0) cc_final: 0.8581 (mt0) REVERT: TH 92 THR cc_start: 0.9594 (m) cc_final: 0.9152 (p) REVERT: TH 112 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: TI 9 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8263 (tp-100) REVERT: TI 29 ASP cc_start: 0.8850 (t0) cc_final: 0.8544 (t0) REVERT: TI 58 ASP cc_start: 0.8813 (t0) cc_final: 0.8476 (t0) REVERT: TI 59 ASP cc_start: 0.9170 (m-30) cc_final: 0.8635 (t0) REVERT: TI 83 GLN cc_start: 0.8956 (mt0) cc_final: 0.8690 (tp40) REVERT: TI 92 THR cc_start: 0.9573 (m) cc_final: 0.9087 (p) REVERT: TI 112 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8714 (mt-10) REVERT: TA 22 SER cc_start: 0.9111 (t) cc_final: 0.8728 (m) REVERT: TA 24 SER cc_start: 0.9058 (m) cc_final: 0.8837 (t) REVERT: TA 38 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8985 (mpp80) REVERT: TA 89 THR cc_start: 0.9176 (m) cc_final: 0.8725 (p) REVERT: TB 7 ASP cc_start: 0.8702 (t0) cc_final: 0.8019 (t0) REVERT: TB 19 SER cc_start: 0.9170 (t) cc_final: 0.8885 (p) REVERT: TB 24 SER cc_start: 0.9137 (m) cc_final: 0.8835 (t) REVERT: TB 27 ASP cc_start: 0.9035 (p0) cc_final: 0.8798 (p0) REVERT: TB 54 THR cc_start: 0.9475 (m) cc_final: 0.9186 (p) REVERT: TB 89 THR cc_start: 0.9104 (m) cc_final: 0.8705 (p) REVERT: TB 189 ASP cc_start: 0.9021 (t0) cc_final: 0.8705 (t0) REVERT: TB 319 MET cc_start: 0.9406 (tmm) cc_final: 0.9054 (tmm) outliers start: 44 outliers final: 20 residues processed: 390 average time/residue: 1.0688 time to fit residues: 467.0422 Evaluate side-chains 362 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 339 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 84 ILE Chi-restraints excluded: chain TD residue 112 GLU 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 TG residue 38 ILE Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TA residue 38 ARG Chi-restraints excluded: chain TA residue 139 THR 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 90 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 148 optimal weight: 0.0370 chunk 62 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 214 HIS TD 80 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 31 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.071059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.060048 restraints weight = 24149.184| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 2.31 r_work: 0.2409 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2290 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14760 Z= 0.130 Angle : 0.483 5.790 20094 Z= 0.269 Chirality : 0.045 0.139 2319 Planarity : 0.003 0.033 2685 Dihedral : 5.987 54.824 2067 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.39 % Allowed : 13.77 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1884 helix: 2.14 (0.32), residues: 264 sheet: 0.26 (0.21), residues: 657 loop : -0.65 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTC 65 HIS 0.003 0.001 HISTB 304 PHE 0.016 0.001 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.005 0.001 ARGTI 95 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 402) hydrogen bonds : angle 4.69211 ( 1110) metal coordination : bond 0.00183 ( 6) covalent geometry : bond 0.00287 (14754) covalent geometry : angle 0.48291 (20094) *********************** 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 394 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 1.554 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8567 (t0) cc_final: 0.8086 (t0) REVERT: TC 22 SER cc_start: 0.9177 (t) cc_final: 0.8692 (m) REVERT: TC 89 THR cc_start: 0.9144 (m) cc_final: 0.8743 (p) REVERT: TC 189 ASP cc_start: 0.8857 (t70) cc_final: 0.8566 (t70) REVERT: TC 199 ASP cc_start: 0.8952 (t0) cc_final: 0.8703 (t0) REVERT: TC 400 ASP cc_start: 0.9288 (t70) cc_final: 0.9070 (t0) REVERT: TD 58 ASP cc_start: 0.8642 (t70) cc_final: 0.8144 (t70) REVERT: TD 63 VAL cc_start: 0.9299 (t) cc_final: 0.8861 (m) REVERT: TD 83 GLN cc_start: 0.8960 (mt0) cc_final: 0.8620 (mt0) REVERT: TD 85 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8719 (mt-10) REVERT: TE 9 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8755 (tp40) REVERT: TE 24 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8495 (mt-10) REVERT: TE 58 ASP cc_start: 0.8910 (t0) cc_final: 0.8637 (t0) REVERT: TE 83 GLN cc_start: 0.9170 (tt0) cc_final: 0.8581 (tt0) REVERT: TE 92 THR cc_start: 0.9521 (m) cc_final: 0.9047 (p) REVERT: TE 112 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8571 (tt0) REVERT: TF 29 ASP cc_start: 0.9029 (t0) cc_final: 0.8799 (t0) REVERT: TF 39 GLU cc_start: 0.8930 (tt0) cc_final: 0.8545 (tt0) REVERT: TF 58 ASP cc_start: 0.8570 (t0) cc_final: 0.7901 (t0) REVERT: TF 59 ASP cc_start: 0.9189 (m-30) cc_final: 0.8605 (t70) REVERT: TF 61 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8598 (mt-10) REVERT: TF 65 ASP cc_start: 0.9048 (t0) cc_final: 0.8841 (t0) REVERT: TF 83 GLN cc_start: 0.9021 (mt0) cc_final: 0.8545 (tt0) REVERT: TF 112 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8433 (mt-10) REVERT: TG 35 PHE cc_start: 0.9531 (m-80) cc_final: 0.9320 (m-80) REVERT: TG 39 GLU cc_start: 0.9018 (tt0) cc_final: 0.8621 (tt0) REVERT: TG 58 ASP cc_start: 0.8841 (t70) cc_final: 0.8282 (t70) REVERT: TG 92 THR cc_start: 0.9627 (m) cc_final: 0.9093 (p) REVERT: TH 58 ASP cc_start: 0.8686 (t0) cc_final: 0.8263 (t0) REVERT: TH 59 ASP cc_start: 0.9237 (m-30) cc_final: 0.8747 (t0) REVERT: TH 83 GLN cc_start: 0.8896 (mt0) cc_final: 0.8425 (mt0) REVERT: TH 85 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8974 (mt-10) REVERT: TH 92 THR cc_start: 0.9582 (m) cc_final: 0.9129 (p) REVERT: TH 112 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: TI 9 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: TI 29 ASP cc_start: 0.8861 (t0) cc_final: 0.8513 (t0) REVERT: TI 58 ASP cc_start: 0.8843 (t0) cc_final: 0.8424 (t0) REVERT: TI 59 ASP cc_start: 0.9177 (m-30) cc_final: 0.8657 (t0) REVERT: TI 83 GLN cc_start: 0.8958 (mt0) cc_final: 0.8612 (tp40) REVERT: TI 92 THR cc_start: 0.9550 (m) cc_final: 0.9064 (p) REVERT: TI 112 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8666 (mt-10) REVERT: TA 22 SER cc_start: 0.9008 (t) cc_final: 0.8629 (m) REVERT: TA 24 SER cc_start: 0.8999 (m) cc_final: 0.8762 (t) REVERT: TA 89 THR cc_start: 0.9181 (m) cc_final: 0.8734 (p) REVERT: TB 19 SER cc_start: 0.9154 (t) cc_final: 0.8876 (p) REVERT: TB 24 SER cc_start: 0.9103 (m) cc_final: 0.8778 (t) REVERT: TB 54 THR cc_start: 0.9422 (m) cc_final: 0.9108 (p) REVERT: TB 89 THR cc_start: 0.9115 (m) cc_final: 0.8730 (p) REVERT: TB 189 ASP cc_start: 0.9052 (t0) cc_final: 0.8737 (t0) REVERT: TB 319 MET cc_start: 0.9437 (tmm) cc_final: 0.9119 (tmm) outliers start: 38 outliers final: 16 residues processed: 374 average time/residue: 1.0590 time to fit residues: 443.9550 Evaluate side-chains 362 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 343 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TD residue 26 LEU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 54 LEU 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 TF residue 62 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TH residue 112 GLU Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 55 THR Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 130 ILE Chi-restraints excluded: chain TA residue 139 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 156 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 0.3980 chunk 188 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.069421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.058389 restraints weight = 24658.598| |-----------------------------------------------------------------------------| r_work (start): 0.2521 rms_B_bonded: 2.30 r_work: 0.2393 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2273 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2686 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= 0.189 Angle : 0.503 6.082 20094 Z= 0.279 Chirality : 0.045 0.147 2319 Planarity : 0.003 0.035 2685 Dihedral : 5.996 54.742 2067 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.14 % Allowed : 14.09 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 1884 helix: 2.12 (0.32), residues: 264 sheet: 0.23 (0.21), residues: 636 loop : -0.64 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPTC 65 HIS 0.004 0.001 HISTA 304 PHE 0.018 0.001 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.004 0.001 ARGTI 95 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 402) hydrogen bonds : angle 4.71388 ( 1110) metal coordination : bond 0.00258 ( 6) covalent geometry : bond 0.00419 (14754) covalent geometry : angle 0.50307 (20094) *********************** 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 399 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 1.682 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8576 (t0) cc_final: 0.8133 (t0) REVERT: TC 22 SER cc_start: 0.9179 (t) cc_final: 0.8700 (m) REVERT: TC 89 THR cc_start: 0.9153 (m) cc_final: 0.8733 (p) REVERT: TC 139 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9163 (t) REVERT: TC 189 ASP cc_start: 0.8970 (t70) cc_final: 0.8609 (t0) REVERT: TC 199 ASP cc_start: 0.8979 (t0) cc_final: 0.8729 (t0) REVERT: TC 400 ASP cc_start: 0.9297 (t70) cc_final: 0.9072 (t0) REVERT: TD 58 ASP cc_start: 0.8677 (t70) cc_final: 0.8146 (t70) REVERT: TD 63 VAL cc_start: 0.9273 (t) cc_final: 0.8790 (m) REVERT: TD 83 GLN cc_start: 0.8970 (mt0) cc_final: 0.8589 (mt0) REVERT: TD 85 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8382 (mt-10) REVERT: TE 9 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (tp40) REVERT: TE 24 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8538 (mt-10) REVERT: TE 58 ASP cc_start: 0.8909 (t0) cc_final: 0.8588 (t0) REVERT: TE 83 GLN cc_start: 0.9184 (tt0) cc_final: 0.8609 (tt0) REVERT: TE 92 THR cc_start: 0.9500 (m) cc_final: 0.9009 (p) REVERT: TF 29 ASP cc_start: 0.9037 (t0) cc_final: 0.8833 (t0) REVERT: TF 58 ASP cc_start: 0.8581 (t0) cc_final: 0.7892 (t0) REVERT: TF 59 ASP cc_start: 0.9176 (m-30) cc_final: 0.8603 (t70) REVERT: TF 61 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8590 (mt-10) REVERT: TF 83 GLN cc_start: 0.9053 (mt0) cc_final: 0.8555 (tt0) REVERT: TF 85 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8363 (mt-10) REVERT: TF 112 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8487 (mt-10) REVERT: TG 39 GLU cc_start: 0.8943 (tt0) cc_final: 0.8537 (tt0) REVERT: TG 52 GLU cc_start: 0.9034 (tt0) cc_final: 0.8779 (tt0) REVERT: TG 58 ASP cc_start: 0.8858 (t70) cc_final: 0.8326 (t70) REVERT: TG 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8852 (t0) REVERT: TG 83 GLN cc_start: 0.9035 (tt0) cc_final: 0.8720 (tt0) REVERT: TG 92 THR cc_start: 0.9609 (m) cc_final: 0.9107 (p) REVERT: TH 24 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8597 (pt0) REVERT: TH 58 ASP cc_start: 0.8725 (t0) cc_final: 0.8274 (t0) REVERT: TH 59 ASP cc_start: 0.9242 (m-30) cc_final: 0.8776 (t0) REVERT: TH 83 GLN cc_start: 0.8892 (mt0) cc_final: 0.8363 (mt0) REVERT: TH 92 THR cc_start: 0.9585 (m) cc_final: 0.9124 (p) REVERT: TH 112 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: TI 9 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8299 (tp-100) REVERT: TI 24 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8501 (mt-10) REVERT: TI 29 ASP cc_start: 0.8903 (t0) cc_final: 0.8517 (t0) REVERT: TI 58 ASP cc_start: 0.8788 (t0) cc_final: 0.8356 (t0) REVERT: TI 59 ASP cc_start: 0.9194 (m-30) cc_final: 0.8668 (t0) REVERT: TI 83 GLN cc_start: 0.9059 (mt0) cc_final: 0.8669 (tp40) REVERT: TI 92 THR cc_start: 0.9534 (m) cc_final: 0.9075 (p) REVERT: TI 112 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8682 (mt-10) REVERT: TA 22 SER cc_start: 0.9035 (t) cc_final: 0.8755 (m) REVERT: TA 24 SER cc_start: 0.9012 (m) cc_final: 0.8771 (t) REVERT: TA 89 THR cc_start: 0.9203 (m) cc_final: 0.8738 (p) REVERT: TB 24 SER cc_start: 0.9149 (m) cc_final: 0.8831 (t) REVERT: TB 54 THR cc_start: 0.9482 (m) cc_final: 0.9191 (p) REVERT: TB 89 THR cc_start: 0.9139 (m) cc_final: 0.8723 (p) REVERT: TB 189 ASP cc_start: 0.9078 (t0) cc_final: 0.8755 (t0) REVERT: TB 319 MET cc_start: 0.9421 (tmm) cc_final: 0.9144 (tmm) outliers start: 50 outliers final: 28 residues processed: 374 average time/residue: 1.0192 time to fit residues: 427.6225 Evaluate side-chains 365 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 333 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 54 LEU 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 27 LEU Chi-restraints excluded: chain TG residue 84 ILE 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 9 GLN Chi-restraints excluded: chain TI residue 55 THR 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 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 173 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TE 31 GLN TE 42 ASN ** TF 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 = 0.2712 r_free = 0.2712 target = 0.067144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.056079 restraints weight = 25054.492| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 2.31 r_work: 0.2344 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2224 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14760 Z= 0.255 Angle : 0.530 5.856 20094 Z= 0.292 Chirality : 0.046 0.155 2319 Planarity : 0.004 0.040 2685 Dihedral : 6.085 54.752 2067 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.40 % Allowed : 14.59 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1884 helix: 2.08 (0.32), residues: 264 sheet: 0.16 (0.21), residues: 636 loop : -0.68 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPTC 65 HIS 0.005 0.001 HISTB 304 PHE 0.020 0.002 PHETA 354 TYR 0.025 0.002 TYRTC 290 ARG 0.004 0.001 ARGTF 111 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 402) hydrogen bonds : angle 4.79907 ( 1110) metal coordination : bond 0.00376 ( 6) covalent geometry : bond 0.00570 (14754) covalent geometry : angle 0.53006 (20094) *********************** 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 400 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 1.793 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8586 (t0) cc_final: 0.8148 (t0) REVERT: TC 89 THR cc_start: 0.9189 (m) cc_final: 0.8765 (p) REVERT: TC 139 THR cc_start: 0.9606 (OUTLIER) cc_final: 0.9174 (t) REVERT: TC 189 ASP cc_start: 0.9012 (t70) cc_final: 0.8575 (t70) REVERT: TC 400 ASP cc_start: 0.9290 (t70) cc_final: 0.9079 (t0) REVERT: TD 24 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8817 (pm20) REVERT: TD 58 ASP cc_start: 0.8766 (t70) cc_final: 0.8257 (t70) REVERT: TD 83 GLN cc_start: 0.9026 (mt0) cc_final: 0.8586 (mt0) REVERT: TD 85 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8487 (mt-10) REVERT: TD 111 ARG cc_start: 0.8964 (mtm-85) cc_final: 0.8738 (mtt90) REVERT: TE 9 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8712 (tp40) REVERT: TE 24 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8551 (mt-10) REVERT: TE 58 ASP cc_start: 0.8908 (t0) cc_final: 0.8583 (t0) REVERT: TE 92 THR cc_start: 0.9485 (m) cc_final: 0.9023 (p) REVERT: TF 29 ASP cc_start: 0.9062 (t0) cc_final: 0.8850 (t0) REVERT: TF 58 ASP cc_start: 0.8608 (t0) cc_final: 0.7904 (t0) REVERT: TF 59 ASP cc_start: 0.9165 (m-30) cc_final: 0.8609 (t70) REVERT: TF 61 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8584 (mt-10) REVERT: TF 83 GLN cc_start: 0.9110 (mt0) cc_final: 0.8672 (mt0) REVERT: TF 85 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8402 (mt-10) REVERT: TF 112 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8521 (mt-10) REVERT: TG 39 GLU cc_start: 0.8987 (tt0) cc_final: 0.8658 (tt0) REVERT: TG 52 GLU cc_start: 0.9047 (tt0) cc_final: 0.8837 (tt0) REVERT: TG 58 ASP cc_start: 0.8851 (t70) cc_final: 0.8348 (t70) REVERT: TG 92 THR cc_start: 0.9636 (m) cc_final: 0.9162 (p) REVERT: TH 52 GLU cc_start: 0.8984 (tt0) cc_final: 0.8642 (tt0) REVERT: TH 58 ASP cc_start: 0.8759 (t0) cc_final: 0.8324 (t0) REVERT: TH 59 ASP cc_start: 0.9232 (m-30) cc_final: 0.8792 (t0) REVERT: TH 83 GLN cc_start: 0.8909 (mt0) cc_final: 0.8381 (mt0) REVERT: TH 92 THR cc_start: 0.9597 (m) cc_final: 0.9156 (p) REVERT: TH 112 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: TI 9 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8580 (tp40) REVERT: TI 24 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8473 (mt-10) REVERT: TI 29 ASP cc_start: 0.8971 (t0) cc_final: 0.8686 (t0) REVERT: TI 52 GLU cc_start: 0.9077 (tt0) cc_final: 0.8772 (tt0) REVERT: TI 58 ASP cc_start: 0.8805 (t0) cc_final: 0.8396 (t0) REVERT: TI 59 ASP cc_start: 0.9199 (m-30) cc_final: 0.8673 (t0) REVERT: TI 83 GLN cc_start: 0.9130 (mt0) cc_final: 0.8629 (tt0) REVERT: TI 92 THR cc_start: 0.9556 (m) cc_final: 0.9127 (p) REVERT: TI 112 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8712 (mt-10) REVERT: TA 22 SER cc_start: 0.9044 (t) cc_final: 0.8758 (m) REVERT: TA 24 SER cc_start: 0.9055 (m) cc_final: 0.8825 (t) REVERT: TA 89 THR cc_start: 0.9274 (m) cc_final: 0.8792 (p) REVERT: TB 24 SER cc_start: 0.9158 (m) cc_final: 0.8831 (t) REVERT: TB 54 THR cc_start: 0.9508 (m) cc_final: 0.9237 (p) REVERT: TB 89 THR cc_start: 0.9156 (m) cc_final: 0.8711 (p) REVERT: TB 189 ASP cc_start: 0.9048 (t0) cc_final: 0.8762 (t0) REVERT: TB 319 MET cc_start: 0.9426 (tmm) cc_final: 0.9135 (tmm) outliers start: 54 outliers final: 31 residues processed: 377 average time/residue: 1.1386 time to fit residues: 480.0904 Evaluate side-chains 374 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 339 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 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 54 LEU 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 TG residue 55 THR 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 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 55 THR 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 315 GLU Chi-restraints excluded: chain TB residue 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 31 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TG 80 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.071873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.060914 restraints weight = 24569.209| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 2.31 r_work: 0.2426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14760 Z= 0.107 Angle : 0.480 7.492 20094 Z= 0.264 Chirality : 0.044 0.139 2319 Planarity : 0.003 0.034 2685 Dihedral : 5.800 53.409 2067 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 16.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 1884 helix: 2.24 (0.32), residues: 264 sheet: 0.08 (0.20), residues: 657 loop : -0.74 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTC 65 HIS 0.002 0.001 HISTA 266 PHE 0.014 0.001 PHETB 354 TYR 0.025 0.001 TYRTC 290 ARG 0.005 0.001 ARGTI 95 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 402) hydrogen bonds : angle 4.61042 ( 1110) metal coordination : bond 0.00124 ( 6) covalent geometry : bond 0.00233 (14754) covalent geometry : angle 0.47963 (20094) *********************** 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 375 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 1.980 Fit side-chains REVERT: TC 22 SER cc_start: 0.9159 (t) cc_final: 0.8673 (m) REVERT: TC 89 THR cc_start: 0.9134 (m) cc_final: 0.8757 (p) REVERT: TC 139 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9130 (t) REVERT: TC 189 ASP cc_start: 0.8982 (t0) cc_final: 0.8570 (t70) REVERT: TC 400 ASP cc_start: 0.9298 (t70) cc_final: 0.9095 (t0) REVERT: TD 58 ASP cc_start: 0.8776 (t70) cc_final: 0.8217 (t70) REVERT: TD 83 GLN cc_start: 0.8920 (mt0) cc_final: 0.8537 (mt0) REVERT: TD 85 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8526 (mt-10) REVERT: TD 92 THR cc_start: 0.9427 (m) cc_final: 0.8944 (p) REVERT: TE 9 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8646 (tp40) REVERT: TE 24 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8531 (mt-10) REVERT: TE 58 ASP cc_start: 0.8910 (t0) cc_final: 0.8590 (t0) REVERT: TE 92 THR cc_start: 0.9491 (m) cc_final: 0.8981 (p) REVERT: TE 112 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8622 (tt0) REVERT: TF 29 ASP cc_start: 0.9043 (t0) cc_final: 0.8825 (t0) REVERT: TF 58 ASP cc_start: 0.8614 (t0) cc_final: 0.7903 (t0) REVERT: TF 59 ASP cc_start: 0.9153 (m-30) cc_final: 0.8629 (t70) REVERT: TF 61 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8562 (mt-10) REVERT: TF 65 ASP cc_start: 0.9067 (t0) cc_final: 0.8866 (t0) REVERT: TF 83 GLN cc_start: 0.9016 (mt0) cc_final: 0.8567 (tt0) REVERT: TF 112 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8506 (mt-10) REVERT: TG 39 GLU cc_start: 0.8901 (tt0) cc_final: 0.8485 (tt0) REVERT: TG 58 ASP cc_start: 0.8809 (t70) cc_final: 0.8306 (t70) REVERT: TG 83 GLN cc_start: 0.8933 (tt0) cc_final: 0.8695 (tt0) REVERT: TG 92 THR cc_start: 0.9601 (m) cc_final: 0.9080 (p) REVERT: TH 24 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8658 (pt0) REVERT: TH 58 ASP cc_start: 0.8702 (t0) cc_final: 0.8221 (t0) REVERT: TH 59 ASP cc_start: 0.9245 (m-30) cc_final: 0.8795 (t0) REVERT: TH 83 GLN cc_start: 0.8765 (mt0) cc_final: 0.8300 (mt0) REVERT: TH 85 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8802 (mt-10) REVERT: TH 92 THR cc_start: 0.9558 (m) cc_final: 0.9053 (p) REVERT: TI 9 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8567 (tp40) REVERT: TI 24 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8460 (mt-10) REVERT: TI 29 ASP cc_start: 0.8864 (t0) cc_final: 0.8568 (t0) REVERT: TI 52 GLU cc_start: 0.9032 (tt0) cc_final: 0.8731 (tt0) REVERT: TI 58 ASP cc_start: 0.8757 (t0) cc_final: 0.8279 (t0) REVERT: TI 59 ASP cc_start: 0.9193 (m-30) cc_final: 0.8656 (t0) REVERT: TI 83 GLN cc_start: 0.9055 (mt0) cc_final: 0.8630 (tp40) REVERT: TI 92 THR cc_start: 0.9536 (m) cc_final: 0.9074 (p) REVERT: TI 112 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8639 (mt-10) REVERT: TA 22 SER cc_start: 0.9025 (t) cc_final: 0.8715 (m) REVERT: TA 24 SER cc_start: 0.8967 (m) cc_final: 0.8755 (t) REVERT: TA 89 THR cc_start: 0.9189 (m) cc_final: 0.8718 (p) REVERT: TB 24 SER cc_start: 0.9145 (m) cc_final: 0.8812 (t) REVERT: TB 54 THR cc_start: 0.9406 (m) cc_final: 0.9113 (p) REVERT: TB 89 THR cc_start: 0.9137 (m) cc_final: 0.8740 (p) REVERT: TB 189 ASP cc_start: 0.9083 (t0) cc_final: 0.8731 (t70) REVERT: TB 287 ARG cc_start: 0.9178 (ttt180) cc_final: 0.8927 (ttt90) REVERT: TB 319 MET cc_start: 0.9442 (tmm) cc_final: 0.9124 (tmm) outliers start: 36 outliers final: 21 residues processed: 358 average time/residue: 1.1174 time to fit residues: 449.2436 Evaluate side-chains 353 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 331 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 GLU Chi-restraints excluded: chain TD residue 27 LEU Chi-restraints excluded: chain TD residue 54 LEU Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 27 LEU Chi-restraints excluded: chain TE residue 54 LEU Chi-restraints excluded: chain TE residue 55 THR 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 27 LEU Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TI residue 55 THR 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 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 100 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 110 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 TE 31 GLN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN TG 42 ASN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 80 GLN TI 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.069377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.058515 restraints weight = 24691.996| |-----------------------------------------------------------------------------| r_work (start): 0.2520 rms_B_bonded: 2.25 r_work: 0.2393 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14760 Z= 0.209 Angle : 0.518 7.263 20094 Z= 0.283 Chirality : 0.045 0.146 2319 Planarity : 0.003 0.037 2685 Dihedral : 5.915 53.653 2067 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.33 % Allowed : 16.92 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1884 helix: 2.20 (0.32), residues: 264 sheet: 0.07 (0.20), residues: 654 loop : -0.76 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTA 65 HIS 0.004 0.001 HISTA 304 PHE 0.018 0.001 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.006 0.001 ARGTA 149 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 402) hydrogen bonds : angle 4.67373 ( 1110) metal coordination : bond 0.00327 ( 6) covalent geometry : bond 0.00470 (14754) covalent geometry : angle 0.51844 (20094) *********************** 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 374 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 1.653 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8578 (t0) cc_final: 0.8129 (t0) REVERT: TC 89 THR cc_start: 0.9169 (m) cc_final: 0.8749 (p) REVERT: TC 139 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9154 (t) REVERT: TC 189 ASP cc_start: 0.9078 (t0) cc_final: 0.8612 (t70) REVERT: TC 400 ASP cc_start: 0.9291 (t70) cc_final: 0.9088 (t0) REVERT: TD 58 ASP cc_start: 0.8848 (t70) cc_final: 0.8325 (t70) REVERT: TD 83 GLN cc_start: 0.8986 (mt0) cc_final: 0.8539 (mt0) REVERT: TD 85 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8505 (mt-10) REVERT: TD 92 THR cc_start: 0.9448 (m) cc_final: 0.8877 (p) REVERT: TD 111 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8698 (mtt90) REVERT: TE 9 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8803 (tp40) REVERT: TE 24 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8542 (mt-10) REVERT: TE 58 ASP cc_start: 0.8911 (t0) cc_final: 0.8556 (t0) REVERT: TE 92 THR cc_start: 0.9500 (m) cc_final: 0.9014 (p) REVERT: TF 58 ASP cc_start: 0.8608 (t0) cc_final: 0.7880 (t0) REVERT: TF 59 ASP cc_start: 0.9132 (m-30) cc_final: 0.8635 (t70) REVERT: TF 61 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8554 (mt-10) REVERT: TF 65 ASP cc_start: 0.9063 (t0) cc_final: 0.8849 (t0) REVERT: TF 83 GLN cc_start: 0.9006 (mt0) cc_final: 0.8441 (tt0) REVERT: TF 85 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8310 (mt-10) REVERT: TF 112 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8487 (mt-10) REVERT: TG 39 GLU cc_start: 0.8921 (tt0) cc_final: 0.8555 (tt0) REVERT: TG 58 ASP cc_start: 0.8821 (t70) cc_final: 0.8311 (t70) REVERT: TG 92 THR cc_start: 0.9634 (m) cc_final: 0.9115 (p) REVERT: TH 24 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8633 (pt0) REVERT: TH 58 ASP cc_start: 0.8717 (t0) cc_final: 0.8226 (t0) REVERT: TH 59 ASP cc_start: 0.9236 (m-30) cc_final: 0.8805 (t0) REVERT: TH 83 GLN cc_start: 0.8824 (mt0) cc_final: 0.8306 (mt0) REVERT: TH 85 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8810 (mt-10) REVERT: TH 92 THR cc_start: 0.9571 (m) cc_final: 0.9093 (p) REVERT: TI 9 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8330 (tp-100) REVERT: TI 24 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8469 (mt-10) REVERT: TI 29 ASP cc_start: 0.8869 (t0) cc_final: 0.8594 (t0) REVERT: TI 58 ASP cc_start: 0.8817 (t0) cc_final: 0.8334 (t0) REVERT: TI 59 ASP cc_start: 0.9193 (m-30) cc_final: 0.8672 (t0) REVERT: TI 83 GLN cc_start: 0.9101 (mt0) cc_final: 0.8653 (tt0) REVERT: TI 92 THR cc_start: 0.9550 (m) cc_final: 0.9122 (p) REVERT: TI 112 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8637 (mt-10) REVERT: TA 22 SER cc_start: 0.9026 (t) cc_final: 0.8708 (m) REVERT: TA 24 SER cc_start: 0.9041 (m) cc_final: 0.8805 (t) REVERT: TA 89 THR cc_start: 0.9225 (m) cc_final: 0.8716 (p) REVERT: TB 24 SER cc_start: 0.9126 (m) cc_final: 0.8785 (t) REVERT: TB 54 THR cc_start: 0.9493 (m) cc_final: 0.9209 (p) REVERT: TB 89 THR cc_start: 0.9153 (m) cc_final: 0.8719 (p) REVERT: TB 189 ASP cc_start: 0.9029 (t0) cc_final: 0.8687 (t0) REVERT: TB 319 MET cc_start: 0.9430 (tmm) cc_final: 0.9148 (tmm) outliers start: 37 outliers final: 27 residues processed: 358 average time/residue: 0.9884 time to fit residues: 398.7586 Evaluate side-chains 367 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 TD residue 27 LEU Chi-restraints excluded: chain TD residue 38 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 54 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 55 THR Chi-restraints excluded: chain TH residue 7 ASN Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 55 THR 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 TA residue 189 ASP Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 339 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 188 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 0.7980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 42 ASN TD 80 GLN TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN TG 42 ASN TG 80 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 80 GLN TI 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.069053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.058119 restraints weight = 24702.725| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.29 r_work: 0.2377 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2258 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14760 Z= 0.206 Angle : 0.522 6.774 20094 Z= 0.285 Chirality : 0.046 0.146 2319 Planarity : 0.003 0.036 2685 Dihedral : 5.951 53.818 2067 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.95 % Allowed : 17.61 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1884 helix: 2.20 (0.32), residues: 264 sheet: 0.02 (0.20), residues: 654 loop : -0.78 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTA 65 HIS 0.004 0.001 HISTB 304 PHE 0.018 0.001 PHETB 354 TYR 0.025 0.002 TYRTC 290 ARG 0.006 0.001 ARGTI 95 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 402) hydrogen bonds : angle 4.70691 ( 1110) metal coordination : bond 0.00297 ( 6) covalent geometry : bond 0.00462 (14754) covalent geometry : angle 0.52216 (20094) *********************** 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 376 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 345 time to evaluate : 1.561 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8581 (t0) cc_final: 0.8128 (t0) REVERT: TC 89 THR cc_start: 0.9164 (m) cc_final: 0.8737 (p) REVERT: TC 139 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9156 (t) REVERT: TC 189 ASP cc_start: 0.9072 (t0) cc_final: 0.8625 (t70) REVERT: TC 400 ASP cc_start: 0.9305 (t70) cc_final: 0.9092 (t0) REVERT: TD 58 ASP cc_start: 0.8847 (t70) cc_final: 0.8323 (t70) REVERT: TD 83 GLN cc_start: 0.8988 (mt0) cc_final: 0.8542 (mt0) REVERT: TD 85 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8444 (mt-10) REVERT: TD 92 THR cc_start: 0.9457 (m) cc_final: 0.8980 (p) REVERT: TD 111 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8722 (mtt90) REVERT: TE 9 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8678 (tp40) REVERT: TE 24 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8525 (mt-10) REVERT: TE 58 ASP cc_start: 0.8908 (t0) cc_final: 0.8534 (t0) REVERT: TE 92 THR cc_start: 0.9499 (m) cc_final: 0.9012 (p) REVERT: TF 29 ASP cc_start: 0.9056 (t0) cc_final: 0.8710 (t0) REVERT: TF 58 ASP cc_start: 0.8583 (t0) cc_final: 0.7846 (t0) REVERT: TF 59 ASP cc_start: 0.9107 (m-30) cc_final: 0.8651 (t70) REVERT: TF 61 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8525 (mt-10) REVERT: TF 65 ASP cc_start: 0.9077 (t0) cc_final: 0.8856 (t0) REVERT: TF 83 GLN cc_start: 0.9002 (mt0) cc_final: 0.8385 (tt0) REVERT: TF 85 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8266 (mt-10) REVERT: TF 112 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8521 (mt-10) REVERT: TG 39 GLU cc_start: 0.8942 (tt0) cc_final: 0.8556 (tt0) REVERT: TG 58 ASP cc_start: 0.8819 (t70) cc_final: 0.8347 (t70) REVERT: TG 65 ASP cc_start: 0.9145 (t0) cc_final: 0.8936 (t0) REVERT: TG 92 THR cc_start: 0.9626 (m) cc_final: 0.9104 (p) REVERT: TH 24 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8614 (pt0) REVERT: TH 52 GLU cc_start: 0.8918 (tt0) cc_final: 0.8561 (tt0) REVERT: TH 58 ASP cc_start: 0.8710 (t0) cc_final: 0.8224 (t0) REVERT: TH 59 ASP cc_start: 0.9229 (m-30) cc_final: 0.8795 (t0) REVERT: TH 83 GLN cc_start: 0.8830 (mt0) cc_final: 0.8365 (mt0) REVERT: TH 92 THR cc_start: 0.9574 (m) cc_final: 0.9101 (p) REVERT: TI 9 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8322 (tp-100) REVERT: TI 24 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8458 (mt-10) REVERT: TI 29 ASP cc_start: 0.8847 (t0) cc_final: 0.8632 (t0) REVERT: TI 58 ASP cc_start: 0.8777 (t0) cc_final: 0.8296 (t0) REVERT: TI 59 ASP cc_start: 0.9172 (m-30) cc_final: 0.8645 (t0) REVERT: TI 83 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: TI 92 THR cc_start: 0.9558 (m) cc_final: 0.9114 (p) REVERT: TI 112 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8644 (mt-10) REVERT: TA 22 SER cc_start: 0.9009 (t) cc_final: 0.8672 (m) REVERT: TA 24 SER cc_start: 0.8999 (m) cc_final: 0.8754 (t) REVERT: TA 89 THR cc_start: 0.9229 (m) cc_final: 0.8725 (p) REVERT: TA 408 ASP cc_start: 0.9170 (t0) cc_final: 0.8955 (t0) REVERT: TB 24 SER cc_start: 0.9121 (m) cc_final: 0.8780 (t) REVERT: TB 54 THR cc_start: 0.9484 (m) cc_final: 0.9199 (p) REVERT: TB 189 ASP cc_start: 0.9030 (t0) cc_final: 0.8715 (t0) REVERT: TB 319 MET cc_start: 0.9422 (tmm) cc_final: 0.9127 (tmm) outliers start: 31 outliers final: 24 residues processed: 363 average time/residue: 0.9316 time to fit residues: 381.2146 Evaluate side-chains 361 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 TD residue 27 LEU 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 54 LEU Chi-restraints excluded: chain TE residue 55 THR 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 55 THR Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 55 THR 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 135 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 Chi-restraints excluded: chain TB residue 339 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 140 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 164 optimal weight: 0.0980 chunk 155 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 80 GLN ** 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 TG 42 ASN TG 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 = 0.2809 r_free = 0.2809 target = 0.071418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.060359 restraints weight = 24589.491| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.32 r_work: 0.2438 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14760 Z= 0.116 Angle : 0.489 6.575 20094 Z= 0.268 Chirality : 0.045 0.142 2319 Planarity : 0.003 0.035 2685 Dihedral : 5.758 53.269 2067 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.89 % Allowed : 17.61 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1884 helix: 2.33 (0.32), residues: 264 sheet: 0.02 (0.20), residues: 654 loop : -0.78 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTC 65 HIS 0.003 0.001 HISTB 304 PHE 0.014 0.001 PHETB 354 TYR 0.024 0.001 TYRTB 290 ARG 0.006 0.000 ARGTI 95 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 402) hydrogen bonds : angle 4.60478 ( 1110) metal coordination : bond 0.00146 ( 6) covalent geometry : bond 0.00261 (14754) covalent geometry : angle 0.48898 (20094) ********************** 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 376 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 346 time to evaluate : 1.757 Fit side-chains REVERT: TC 22 SER cc_start: 0.9245 (t) cc_final: 0.8720 (m) REVERT: TC 89 THR cc_start: 0.9129 (m) cc_final: 0.8753 (p) REVERT: TC 139 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9110 (t) REVERT: TC 189 ASP cc_start: 0.8995 (t0) cc_final: 0.8548 (t70) REVERT: TD 58 ASP cc_start: 0.8881 (t70) cc_final: 0.8581 (t70) REVERT: TD 83 GLN cc_start: 0.8952 (mt0) cc_final: 0.8576 (mt0) REVERT: TD 85 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8433 (mt-10) REVERT: TD 92 THR cc_start: 0.9452 (m) cc_final: 0.8933 (p) REVERT: TE 9 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8775 (tp40) REVERT: TE 24 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8521 (mt-10) REVERT: TE 58 ASP cc_start: 0.8927 (t0) cc_final: 0.8541 (t0) REVERT: TE 92 THR cc_start: 0.9483 (m) cc_final: 0.8973 (p) REVERT: TE 112 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8574 (tt0) REVERT: TF 29 ASP cc_start: 0.9002 (t0) cc_final: 0.8705 (t0) REVERT: TF 31 GLN cc_start: 0.9190 (mt0) cc_final: 0.8927 (mt0) REVERT: TF 58 ASP cc_start: 0.8537 (t0) cc_final: 0.7929 (t0) REVERT: TF 59 ASP cc_start: 0.9156 (m-30) cc_final: 0.8836 (t70) REVERT: TF 61 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8599 (mt-10) REVERT: TF 65 ASP cc_start: 0.9054 (t0) cc_final: 0.8813 (t0) REVERT: TF 83 GLN cc_start: 0.8989 (mt0) cc_final: 0.8335 (tt0) REVERT: TF 85 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8354 (mt-10) REVERT: TF 112 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8510 (mt-10) REVERT: TG 39 GLU cc_start: 0.8909 (tt0) cc_final: 0.8448 (tt0) REVERT: TG 58 ASP cc_start: 0.8863 (t70) cc_final: 0.8366 (t70) REVERT: TG 65 ASP cc_start: 0.9159 (t0) cc_final: 0.8908 (t0) REVERT: TG 83 GLN cc_start: 0.8972 (tt0) cc_final: 0.8635 (tt0) REVERT: TG 92 THR cc_start: 0.9595 (m) cc_final: 0.9097 (p) REVERT: TH 58 ASP cc_start: 0.8723 (t0) cc_final: 0.8234 (t0) REVERT: TH 59 ASP cc_start: 0.9233 (m-30) cc_final: 0.8800 (t0) REVERT: TH 83 GLN cc_start: 0.8799 (mt0) cc_final: 0.8220 (mt0) REVERT: TH 85 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8979 (mt-10) REVERT: TH 92 THR cc_start: 0.9563 (m) cc_final: 0.9079 (p) REVERT: TI 9 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8543 (tp40) REVERT: TI 24 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8446 (mt-10) REVERT: TI 29 ASP cc_start: 0.8811 (t0) cc_final: 0.8555 (t0) REVERT: TI 58 ASP cc_start: 0.8788 (t0) cc_final: 0.8284 (t0) REVERT: TI 59 ASP cc_start: 0.9250 (m-30) cc_final: 0.8741 (t0) REVERT: TI 83 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: TI 92 THR cc_start: 0.9543 (m) cc_final: 0.9080 (p) REVERT: TI 112 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8621 (mt-10) REVERT: TA 22 SER cc_start: 0.9019 (t) cc_final: 0.8674 (m) REVERT: TA 24 SER cc_start: 0.8970 (m) cc_final: 0.8746 (t) REVERT: TA 89 THR cc_start: 0.9206 (m) cc_final: 0.8719 (p) REVERT: TA 287 ARG cc_start: 0.9259 (ttt180) cc_final: 0.9001 (ttt90) REVERT: TB 24 SER cc_start: 0.9121 (m) cc_final: 0.8784 (t) REVERT: TB 54 THR cc_start: 0.9460 (m) cc_final: 0.9152 (p) REVERT: TB 189 ASP cc_start: 0.9092 (t0) cc_final: 0.8685 (t70) REVERT: TB 287 ARG cc_start: 0.9152 (ttt180) cc_final: 0.8939 (ttt90) REVERT: TB 319 MET cc_start: 0.9434 (tmm) cc_final: 0.9162 (tmm) outliers start: 30 outliers final: 21 residues processed: 370 average time/residue: 1.1338 time to fit residues: 471.2777 Evaluate side-chains 358 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 TD residue 27 LEU 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 54 LEU Chi-restraints excluded: chain TE residue 55 THR 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 TH residue 55 THR Chi-restraints excluded: chain TI residue 55 THR Chi-restraints excluded: chain TI residue 83 GLN Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 135 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 132 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 53 optimal weight: 0.0040 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TE 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN TG 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 = 0.2782 r_free = 0.2782 target = 0.070019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.059033 restraints weight = 24716.968| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 2.29 r_work: 0.2410 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2292 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14760 Z= 0.172 Angle : 0.513 6.211 20094 Z= 0.280 Chirality : 0.045 0.148 2319 Planarity : 0.003 0.036 2685 Dihedral : 5.834 53.380 2067 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.70 % Allowed : 17.86 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1884 helix: 2.35 (0.32), residues: 261 sheet: -0.03 (0.20), residues: 654 loop : -0.78 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTA 65 HIS 0.003 0.001 HISTB 304 PHE 0.017 0.001 PHETB 354 TYR 0.025 0.002 TYRTC 290 ARG 0.006 0.001 ARGTA 149 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 402) hydrogen bonds : angle 4.65175 ( 1110) metal coordination : bond 0.00232 ( 6) covalent geometry : bond 0.00391 (14754) covalent geometry : angle 0.51279 (20094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12408.31 seconds wall clock time: 215 minutes 26.97 seconds (12926.97 seconds total)