Starting phenix.real_space_refine on Sun Nov 17 20:07:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_18550.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_18550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_18550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_18550.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qpg_18550/11_2024/8qpg_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-5513/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: 9.68, per 1000 atoms: 0.67 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: 3.61 Conformation dependent library (CDL) restraints added in 2.4 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: 1.68 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: 4.38 Time building geometry restraints manager: 4.12 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: 0.00 Found NCS groups: ncs_group { reference = chain 'TA' selection = chain 'TB' selection = chain 'TC' } ncs_group { reference = chain 'TD' selection = chain 'TE' selection = chain 'TF' selection = chain 'TG' selection = chain 'TH' selection = chain 'TI' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.820 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.990 ------------------------------------------------------------------------------- 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 : 0.008 0.104 14754 Z= 0.550 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 *********************** 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 : 1.677 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8520 (t0) cc_final: 0.8083 (t0) REVERT: TC 194 ASP cc_start: 0.8793 (t70) cc_final: 0.8342 (t70) REVERT: TC 408 ASP cc_start: 0.8675 (t0) cc_final: 0.8463 (t0) REVERT: TD 55 THR cc_start: 0.9522 (m) cc_final: 0.9198 (p) REVERT: TD 59 ASP cc_start: 0.8937 (m-30) cc_final: 0.8433 (t0) REVERT: TD 63 VAL cc_start: 0.9722 (t) cc_final: 0.9487 (m) REVERT: TD 71 ASP cc_start: 0.8857 (t0) cc_final: 0.8579 (t0) REVERT: TD 83 GLN cc_start: 0.8884 (mt0) cc_final: 0.8604 (tt0) REVERT: TD 92 THR cc_start: 0.9490 (m) cc_final: 0.9209 (p) REVERT: TE 55 THR cc_start: 0.9348 (m) cc_final: 0.9068 (p) REVERT: TE 59 ASP cc_start: 0.9008 (m-30) cc_final: 0.8669 (t0) REVERT: TE 63 VAL cc_start: 0.9416 (t) cc_final: 0.9135 (m) REVERT: TE 92 THR cc_start: 0.9438 (m) cc_final: 0.9129 (p) REVERT: TF 29 ASP cc_start: 0.8945 (t0) cc_final: 0.8670 (t0) REVERT: TF 55 THR cc_start: 0.9500 (m) cc_final: 0.9250 (p) REVERT: TF 59 ASP cc_start: 0.9039 (m-30) cc_final: 0.8760 (t70) REVERT: TF 63 VAL cc_start: 0.9710 (t) cc_final: 0.9500 (m) REVERT: TF 83 GLN cc_start: 0.8966 (mt0) cc_final: 0.8702 (mt0) REVERT: TF 92 THR cc_start: 0.9492 (m) cc_final: 0.9276 (p) REVERT: TF 112 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8405 (mt-10) REVERT: TG 55 THR cc_start: 0.9420 (m) cc_final: 0.9117 (p) REVERT: TG 58 ASP cc_start: 0.8894 (t70) cc_final: 0.8631 (t0) REVERT: TG 59 ASP cc_start: 0.8978 (m-30) cc_final: 0.8541 (t0) REVERT: TG 63 VAL cc_start: 0.9466 (t) cc_final: 0.9184 (m) REVERT: TG 65 ASP cc_start: 0.8426 (t0) cc_final: 0.8066 (t0) REVERT: TG 71 ASP cc_start: 0.9045 (t0) cc_final: 0.8740 (t0) REVERT: TG 92 THR cc_start: 0.9534 (m) cc_final: 0.9216 (p) REVERT: TH 55 THR cc_start: 0.9572 (m) cc_final: 0.9252 (p) REVERT: TH 59 ASP cc_start: 0.8936 (m-30) cc_final: 0.8542 (t0) REVERT: TH 63 VAL cc_start: 0.9695 (t) cc_final: 0.9442 (m) REVERT: TH 83 GLN cc_start: 0.8903 (mt0) cc_final: 0.8464 (mt0) REVERT: TH 92 THR cc_start: 0.9423 (m) cc_final: 0.9153 (p) REVERT: TI 29 ASP cc_start: 0.8843 (t0) cc_final: 0.8492 (t0) REVERT: TI 55 THR cc_start: 0.9432 (m) cc_final: 0.9127 (p) REVERT: TI 59 ASP cc_start: 0.8968 (m-30) cc_final: 0.8586 (t0) REVERT: TI 63 VAL cc_start: 0.9415 (t) cc_final: 0.9120 (m) REVERT: TI 92 THR cc_start: 0.9528 (m) cc_final: 0.9256 (p) REVERT: TI 112 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8504 (mt-10) REVERT: TA 408 ASP cc_start: 0.8683 (t0) cc_final: 0.8357 (t0) REVERT: TB 7 ASP cc_start: 0.8662 (t0) cc_final: 0.8387 (t0) REVERT: TB 194 ASP cc_start: 0.8848 (t70) cc_final: 0.8471 (t70) REVERT: TB 319 MET cc_start: 0.8881 (tmm) cc_final: 0.8607 (tmm) outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 0.9220 time to fit residues: 552.1673 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 : 1.795 ------------------------------------------------------------------------------- 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: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14754 Z= 0.242 Angle : 0.551 6.165 20094 Z= 0.311 Chirality : 0.046 0.151 2319 Planarity : 0.003 0.038 2685 Dihedral : 6.717 55.570 2067 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.58 % Allowed : 10.57 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1884 helix: 1.60 (0.31), residues: 261 sheet: 0.57 (0.20), residues: 669 loop : -0.67 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPTC 65 HIS 0.004 0.001 HISTA 324 PHE 0.021 0.002 PHETA 354 TYR 0.029 0.002 TYRTB 290 ARG 0.008 0.001 ARGTB 52 *********************** 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 442 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 401 time to evaluate : 1.709 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8669 (t0) cc_final: 0.8354 (t0) REVERT: TC 89 THR cc_start: 0.9263 (m) cc_final: 0.8937 (p) REVERT: TD 63 VAL cc_start: 0.9564 (t) cc_final: 0.9292 (m) REVERT: TD 71 ASP cc_start: 0.8915 (t0) cc_final: 0.8663 (t0) REVERT: TD 83 GLN cc_start: 0.8781 (mt0) cc_final: 0.8515 (mt0) REVERT: TD 85 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8778 (mt-10) REVERT: TD 92 THR cc_start: 0.9437 (m) cc_final: 0.9115 (p) REVERT: TE 59 ASP cc_start: 0.9016 (m-30) cc_final: 0.8633 (t0) REVERT: TE 92 THR cc_start: 0.9481 (m) cc_final: 0.9200 (p) REVERT: TF 29 ASP cc_start: 0.8897 (t0) cc_final: 0.8688 (t0) REVERT: TF 39 GLU cc_start: 0.8607 (tt0) cc_final: 0.8019 (tt0) REVERT: TF 58 ASP cc_start: 0.8771 (t0) cc_final: 0.8476 (t0) REVERT: TF 59 ASP cc_start: 0.9184 (m-30) cc_final: 0.8815 (t70) REVERT: TF 63 VAL cc_start: 0.9625 (t) cc_final: 0.9403 (m) REVERT: TF 83 GLN cc_start: 0.8811 (mt0) cc_final: 0.8478 (tt0) REVERT: TF 92 THR cc_start: 0.9443 (m) cc_final: 0.9183 (p) REVERT: TF 112 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8367 (mt-10) REVERT: TG 39 GLU cc_start: 0.8673 (tt0) cc_final: 0.8429 (tt0) REVERT: TG 58 ASP cc_start: 0.8983 (t70) cc_final: 0.8742 (t0) REVERT: TG 63 VAL cc_start: 0.9303 (t) cc_final: 0.8951 (m) REVERT: TG 92 THR cc_start: 0.9519 (m) cc_final: 0.9276 (p) REVERT: TH 59 ASP cc_start: 0.9023 (m-30) cc_final: 0.8744 (t0) REVERT: TH 78 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9320 (tt) REVERT: TI 29 ASP cc_start: 0.8731 (t0) cc_final: 0.8473 (t0) REVERT: TI 59 ASP cc_start: 0.9058 (m-30) cc_final: 0.8826 (t0) REVERT: TI 63 VAL cc_start: 0.9330 (t) cc_final: 0.8991 (m) REVERT: TI 83 GLN cc_start: 0.8870 (mt0) cc_final: 0.8612 (tt0) REVERT: TI 92 THR cc_start: 0.9478 (m) cc_final: 0.9249 (p) REVERT: TA 69 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9070 (tp) REVERT: TA 89 THR cc_start: 0.9302 (m) cc_final: 0.9013 (p) REVERT: TB 89 THR cc_start: 0.9248 (m) cc_final: 0.9009 (p) REVERT: TB 319 MET cc_start: 0.8868 (tmm) cc_final: 0.8641 (tmm) outliers start: 41 outliers final: 14 residues processed: 419 average time/residue: 1.0051 time to fit residues: 474.3801 Evaluate side-chains 353 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 337 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 TD residue 38 ILE Chi-restraints excluded: chain TD residue 84 ILE Chi-restraints excluded: chain TE residue 27 LEU Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TH residue 78 ILE Chi-restraints excluded: chain TI residue 27 LEU 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 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.0050 chunk 142 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 153 optimal weight: 0.0770 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 overall best weight: 1.2156 ------------------------------------------------------------------------------- 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 TE 42 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14754 Z= 0.180 Angle : 0.503 7.324 20094 Z= 0.281 Chirality : 0.045 0.140 2319 Planarity : 0.003 0.032 2685 Dihedral : 6.136 55.448 2067 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.77 % Allowed : 12.33 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.19), residues: 1884 helix: 2.01 (0.32), residues: 264 sheet: 0.39 (0.21), residues: 639 loop : -0.60 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPTC 65 HIS 0.003 0.001 HISTB 304 PHE 0.016 0.001 PHETA 354 TYR 0.026 0.002 TYRTC 290 ARG 0.005 0.001 ARGTA 133 *********************** 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 413 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 369 time to evaluate : 1.704 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8561 (t0) cc_final: 0.8239 (t0) REVERT: TC 89 THR cc_start: 0.9235 (m) cc_final: 0.9001 (p) REVERT: TC 217 ASP cc_start: 0.8877 (m-30) cc_final: 0.8417 (m-30) REVERT: TD 63 VAL cc_start: 0.9560 (t) cc_final: 0.9221 (m) REVERT: TD 71 ASP cc_start: 0.8920 (t0) cc_final: 0.8671 (t0) REVERT: TD 85 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8816 (mt-10) REVERT: TD 92 THR cc_start: 0.9403 (m) cc_final: 0.9057 (p) REVERT: TE 59 ASP cc_start: 0.9037 (m-30) cc_final: 0.8789 (t0) REVERT: TE 83 GLN cc_start: 0.8976 (tt0) cc_final: 0.8587 (tp40) REVERT: TE 85 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8741 (mt-10) REVERT: TE 92 THR cc_start: 0.9407 (m) cc_final: 0.9105 (p) REVERT: TF 39 GLU cc_start: 0.8598 (tt0) cc_final: 0.8180 (tt0) REVERT: TF 58 ASP cc_start: 0.8764 (t0) cc_final: 0.8393 (t0) REVERT: TF 59 ASP cc_start: 0.9111 (m-30) cc_final: 0.8736 (t70) REVERT: TF 112 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8283 (mt-10) REVERT: TG 58 ASP cc_start: 0.9019 (t70) cc_final: 0.8707 (t0) REVERT: TG 92 THR cc_start: 0.9494 (m) cc_final: 0.9174 (p) REVERT: TI 9 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8817 (tp40) REVERT: TI 58 ASP cc_start: 0.8922 (t0) cc_final: 0.8589 (t0) REVERT: TI 59 ASP cc_start: 0.9046 (m-30) cc_final: 0.8792 (t0) REVERT: TI 92 THR cc_start: 0.9443 (m) cc_final: 0.9181 (p) REVERT: TA 89 THR cc_start: 0.9294 (m) cc_final: 0.9006 (p) REVERT: TB 89 THR cc_start: 0.9225 (m) cc_final: 0.8982 (p) REVERT: TB 319 MET cc_start: 0.8931 (tmm) cc_final: 0.8697 (tmm) outliers start: 44 outliers final: 16 residues processed: 391 average time/residue: 1.0547 time to fit residues: 462.8164 Evaluate side-chains 348 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 331 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 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 TG residue 84 ILE Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TA residue 130 ILE 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 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TC 214 HIS TD 31 GLN TD 80 GLN TE 31 GLN TE 82 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TH 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14754 Z= 0.492 Angle : 0.587 6.252 20094 Z= 0.323 Chirality : 0.047 0.166 2319 Planarity : 0.004 0.049 2685 Dihedral : 6.351 56.316 2067 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.52 % Allowed : 12.96 % Favored : 83.52 % Cbeta Deviations : 0.00 % 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: 0.01 (0.19), residues: 1884 helix: 1.93 (0.32), residues: 264 sheet: 0.12 (0.21), residues: 666 loop : -0.58 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPTC 65 HIS 0.007 0.002 HISTB 304 PHE 0.023 0.002 PHETA 354 TYR 0.026 0.002 TYRTB 290 ARG 0.005 0.001 ARGTI 95 *********************** 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 404 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 2.112 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8630 (t0) cc_final: 0.8280 (t0) REVERT: TC 89 THR cc_start: 0.9303 (m) cc_final: 0.8980 (p) REVERT: TC 217 ASP cc_start: 0.8930 (m-30) cc_final: 0.8535 (m-30) REVERT: TD 83 GLN cc_start: 0.9073 (tt0) cc_final: 0.8796 (tt0) REVERT: TD 85 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8538 (mt-10) REVERT: TE 83 GLN cc_start: 0.9149 (tt0) cc_final: 0.8760 (tt0) REVERT: TE 92 THR cc_start: 0.9417 (m) cc_final: 0.9185 (p) REVERT: TF 58 ASP cc_start: 0.8776 (t0) cc_final: 0.8375 (t0) REVERT: TF 59 ASP cc_start: 0.9075 (m-30) cc_final: 0.8794 (t70) REVERT: TF 83 GLN cc_start: 0.9046 (tt0) cc_final: 0.8808 (tt0) REVERT: TF 85 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8464 (mt-10) REVERT: TF 112 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8369 (mt-10) REVERT: TG 58 ASP cc_start: 0.9037 (t70) cc_final: 0.8752 (t70) REVERT: TG 92 THR cc_start: 0.9556 (m) cc_final: 0.9325 (p) REVERT: TI 9 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8720 (tp-100) REVERT: TI 58 ASP cc_start: 0.8983 (t0) cc_final: 0.8665 (t0) REVERT: TI 59 ASP cc_start: 0.9055 (m-30) cc_final: 0.8804 (t0) REVERT: TI 65 ASP cc_start: 0.9024 (t0) cc_final: 0.8685 (t0) REVERT: TI 92 THR cc_start: 0.9454 (m) cc_final: 0.9215 (p) REVERT: TA 89 THR cc_start: 0.9382 (m) cc_final: 0.9051 (p) REVERT: TB 89 THR cc_start: 0.9324 (m) cc_final: 0.9003 (p) REVERT: TB 319 MET cc_start: 0.8930 (tmm) cc_final: 0.8675 (tmm) outliers start: 56 outliers final: 33 residues processed: 380 average time/residue: 1.0820 time to fit residues: 459.5849 Evaluate side-chains 365 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 331 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 16 SER Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 168 THR Chi-restraints excluded: chain 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 9 GLN Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TF residue 40 ILE Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TG residue 38 ILE Chi-restraints excluded: chain TG residue 84 ILE Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 34 LYS 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 116 LEU 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 81 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 42 ASN TD 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 31 GLN TF 80 GLN ** TG 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TG 80 GLN TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14754 Z= 0.241 Angle : 0.516 7.323 20094 Z= 0.285 Chirality : 0.045 0.157 2319 Planarity : 0.003 0.036 2685 Dihedral : 6.103 55.092 2067 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 14.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1884 helix: 2.12 (0.32), residues: 264 sheet: 0.18 (0.21), residues: 636 loop : -0.66 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPTC 65 HIS 0.003 0.001 HISTA 304 PHE 0.017 0.001 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.006 0.001 ARGTI 95 *********************** 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 383 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 1.777 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8556 (t0) cc_final: 0.8252 (t0) REVERT: TC 89 THR cc_start: 0.9281 (m) cc_final: 0.8975 (p) REVERT: TD 83 GLN cc_start: 0.9062 (tt0) cc_final: 0.8765 (tt0) REVERT: TD 85 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8573 (mt-10) REVERT: TE 9 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8848 (tp40) REVERT: TE 83 GLN cc_start: 0.9105 (tt0) cc_final: 0.8666 (tt0) REVERT: TE 92 THR cc_start: 0.9425 (m) cc_final: 0.9170 (p) REVERT: TF 58 ASP cc_start: 0.8755 (t0) cc_final: 0.8370 (t0) REVERT: TF 59 ASP cc_start: 0.9054 (m-30) cc_final: 0.8803 (t70) REVERT: TF 112 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8333 (mt-10) REVERT: TG 58 ASP cc_start: 0.9038 (t70) cc_final: 0.8761 (t70) REVERT: TG 92 THR cc_start: 0.9523 (m) cc_final: 0.9264 (p) REVERT: TH 58 ASP cc_start: 0.8826 (t0) cc_final: 0.8604 (t70) REVERT: TI 9 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8776 (tp40) REVERT: TI 58 ASP cc_start: 0.8964 (t0) cc_final: 0.8574 (t0) REVERT: TI 59 ASP cc_start: 0.9039 (m-30) cc_final: 0.8804 (t0) REVERT: TI 92 THR cc_start: 0.9465 (m) cc_final: 0.9231 (p) REVERT: TA 89 THR cc_start: 0.9382 (m) cc_final: 0.9049 (p) REVERT: TB 89 THR cc_start: 0.9294 (m) cc_final: 0.9016 (p) REVERT: TB 319 MET cc_start: 0.8965 (tmm) cc_final: 0.8731 (tmm) outliers start: 44 outliers final: 23 residues processed: 358 average time/residue: 1.1048 time to fit residues: 441.4218 Evaluate side-chains 352 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 164 GLU 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 84 ILE Chi-restraints excluded: chain TE residue 9 GLN Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 27 LEU Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 34 LYS Chi-restraints excluded: chain TI residue 55 THR Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 116 LEU Chi-restraints excluded: chain TA residue 139 THR 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 339 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 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 TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14754 Z= 0.353 Angle : 0.539 7.099 20094 Z= 0.296 Chirality : 0.046 0.154 2319 Planarity : 0.003 0.039 2685 Dihedral : 6.125 54.428 2067 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.96 % Allowed : 15.22 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1884 helix: 2.08 (0.32), residues: 264 sheet: 0.07 (0.21), residues: 636 loop : -0.69 (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 0.019 0.002 PHETA 354 TYR 0.025 0.002 TYRTC 290 ARG 0.005 0.001 ARGTI 95 *********************** 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 376 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 1.727 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8573 (t0) cc_final: 0.8282 (t0) REVERT: TC 89 THR cc_start: 0.9291 (m) cc_final: 0.8989 (p) REVERT: TC 139 THR cc_start: 0.9677 (OUTLIER) cc_final: 0.9240 (t) REVERT: TD 83 GLN cc_start: 0.9065 (tt0) cc_final: 0.8762 (tt0) REVERT: TD 85 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8623 (mt-10) REVERT: TE 9 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8907 (tp40) REVERT: TE 92 THR cc_start: 0.9419 (m) cc_final: 0.9169 (p) REVERT: TF 58 ASP cc_start: 0.8748 (t0) cc_final: 0.8311 (t0) REVERT: TF 59 ASP cc_start: 0.9049 (m-30) cc_final: 0.8786 (t70) REVERT: TF 61 GLU cc_start: 0.8526 (mp0) cc_final: 0.8284 (mp0) REVERT: TF 83 GLN cc_start: 0.8984 (tt0) cc_final: 0.8779 (tt0) REVERT: TF 112 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8382 (mt-10) REVERT: TG 58 ASP cc_start: 0.9028 (t70) cc_final: 0.8762 (t70) REVERT: TG 92 THR cc_start: 0.9531 (m) cc_final: 0.9279 (p) REVERT: TI 9 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8648 (tp-100) REVERT: TI 58 ASP cc_start: 0.8993 (t0) cc_final: 0.8595 (t0) REVERT: TI 59 ASP cc_start: 0.9045 (m-30) cc_final: 0.8794 (t0) REVERT: TI 92 THR cc_start: 0.9472 (m) cc_final: 0.9254 (p) REVERT: TA 89 THR cc_start: 0.9426 (m) cc_final: 0.9090 (p) REVERT: TB 319 MET cc_start: 0.8937 (tmm) cc_final: 0.8679 (tmm) outliers start: 47 outliers final: 28 residues processed: 351 average time/residue: 1.1947 time to fit residues: 467.5097 Evaluate side-chains 345 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 164 GLU 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 84 ILE Chi-restraints excluded: chain TD residue 112 GLU Chi-restraints excluded: chain TE residue 9 GLN 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 55 THR Chi-restraints excluded: chain TH residue 64 GLU Chi-restraints excluded: chain TH residue 113 VAL Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 34 LYS 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 116 LEU Chi-restraints excluded: chain TA residue 139 THR 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 339 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- 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 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 80 GLN TG 80 GLN TH 31 GLN TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14754 Z= 0.434 Angle : 0.568 6.867 20094 Z= 0.311 Chirality : 0.047 0.168 2319 Planarity : 0.004 0.045 2685 Dihedral : 6.219 54.224 2067 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.46 % Allowed : 15.09 % 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: -0.15 (0.19), residues: 1884 helix: 2.09 (0.31), residues: 261 sheet: 0.03 (0.21), residues: 636 loop : -0.76 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPTC 65 HIS 0.006 0.001 HISTA 304 PHE 0.021 0.002 PHETA 354 TYR 0.025 0.002 TYRTC 290 ARG 0.008 0.001 ARGTI 95 *********************** 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 378 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 1.724 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8586 (t0) cc_final: 0.8300 (t0) REVERT: TC 89 THR cc_start: 0.9296 (m) cc_final: 0.8988 (p) REVERT: TC 139 THR cc_start: 0.9674 (OUTLIER) cc_final: 0.9252 (t) REVERT: TC 164 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: TD 83 GLN cc_start: 0.9085 (tt0) cc_final: 0.8768 (tt0) REVERT: TD 85 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8648 (mt-10) REVERT: TE 92 THR cc_start: 0.9426 (m) cc_final: 0.9207 (p) REVERT: TF 58 ASP cc_start: 0.8779 (t0) cc_final: 0.8330 (t0) REVERT: TF 59 ASP cc_start: 0.9048 (m-30) cc_final: 0.8799 (t70) REVERT: TF 61 GLU cc_start: 0.8572 (mp0) cc_final: 0.8306 (mp0) REVERT: TF 83 GLN cc_start: 0.9008 (tt0) cc_final: 0.8655 (tt0) REVERT: TF 85 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8484 (mt-10) REVERT: TF 112 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8395 (mt-10) REVERT: TG 58 ASP cc_start: 0.9037 (t70) cc_final: 0.8753 (t70) REVERT: TG 92 THR cc_start: 0.9527 (m) cc_final: 0.9283 (p) REVERT: TI 9 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8789 (tp40) REVERT: TI 58 ASP cc_start: 0.8987 (t0) cc_final: 0.8563 (t0) REVERT: TI 59 ASP cc_start: 0.9040 (m-30) cc_final: 0.8794 (t0) REVERT: TI 92 THR cc_start: 0.9479 (m) cc_final: 0.9271 (p) REVERT: TA 89 THR cc_start: 0.9437 (m) cc_final: 0.9091 (p) REVERT: TB 164 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: TB 319 MET cc_start: 0.8929 (tmm) cc_final: 0.8668 (tmm) outliers start: 55 outliers final: 37 residues processed: 353 average time/residue: 1.1209 time to fit residues: 440.4474 Evaluate side-chains 363 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain TC residue 19 SER Chi-restraints excluded: chain TC residue 95 VAL Chi-restraints excluded: chain TC residue 135 VAL Chi-restraints excluded: chain TC residue 139 THR Chi-restraints excluded: chain TC residue 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 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 TG residue 84 ILE Chi-restraints excluded: chain TH residue 7 ASN Chi-restraints excluded: chain TH residue 38 ILE Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 64 GLU Chi-restraints excluded: chain TH residue 113 VAL Chi-restraints excluded: chain TI residue 9 GLN Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 34 LYS 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 116 LEU Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TA residue 164 GLU Chi-restraints excluded: chain TA residue 168 THR Chi-restraints excluded: chain TB residue 19 SER Chi-restraints excluded: chain TB residue 24 SER Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 164 GLU 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 112 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 80 GLN ** TE 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TE 42 ASN TF 80 GLN TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14754 Z= 0.233 Angle : 0.521 7.304 20094 Z= 0.285 Chirality : 0.045 0.146 2319 Planarity : 0.003 0.036 2685 Dihedral : 6.020 54.222 2067 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.64 % Allowed : 16.79 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.19), residues: 1884 helix: 2.24 (0.32), residues: 261 sheet: -0.00 (0.20), residues: 648 loop : -0.83 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPTC 65 HIS 0.005 0.001 HISTI 41 PHE 0.017 0.001 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.007 0.001 ARGTI 95 *********************** 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 367 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 1.631 Fit side-chains REVERT: TC 89 THR cc_start: 0.9269 (m) cc_final: 0.8953 (p) REVERT: TC 139 THR cc_start: 0.9631 (OUTLIER) cc_final: 0.9196 (t) REVERT: TD 83 GLN cc_start: 0.9061 (tt0) cc_final: 0.8764 (tt0) REVERT: TD 85 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8632 (mt-10) REVERT: TE 9 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8781 (tp-100) REVERT: TE 92 THR cc_start: 0.9426 (m) cc_final: 0.9192 (p) REVERT: TF 58 ASP cc_start: 0.8753 (t0) cc_final: 0.8316 (t0) REVERT: TF 59 ASP cc_start: 0.9033 (m-30) cc_final: 0.8787 (t70) REVERT: TF 61 GLU cc_start: 0.8546 (mp0) cc_final: 0.8258 (mp0) REVERT: TF 112 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8341 (mt-10) REVERT: TG 58 ASP cc_start: 0.9036 (t70) cc_final: 0.8773 (t70) REVERT: TG 92 THR cc_start: 0.9501 (m) cc_final: 0.9210 (p) REVERT: TH 59 ASP cc_start: 0.9066 (m-30) cc_final: 0.8660 (t0) REVERT: TI 9 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8684 (tp-100) REVERT: TI 58 ASP cc_start: 0.8961 (t0) cc_final: 0.8525 (t0) REVERT: TI 59 ASP cc_start: 0.9047 (m-30) cc_final: 0.8807 (t0) REVERT: TI 92 THR cc_start: 0.9463 (m) cc_final: 0.9237 (p) REVERT: TA 89 THR cc_start: 0.9439 (m) cc_final: 0.9104 (p) REVERT: TB 164 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: TB 319 MET cc_start: 0.8966 (tmm) cc_final: 0.8738 (tmm) outliers start: 42 outliers final: 29 residues processed: 347 average time/residue: 1.0892 time to fit residues: 422.2025 Evaluate side-chains 342 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 40 ILE 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 54 LEU Chi-restraints excluded: chain TE residue 113 VAL Chi-restraints excluded: chain TF residue 27 LEU Chi-restraints excluded: chain TF residue 62 LEU Chi-restraints excluded: chain TG residue 26 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 27 LEU Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 64 GLU Chi-restraints excluded: chain TH residue 113 VAL Chi-restraints excluded: chain TI residue 27 LEU Chi-restraints excluded: chain TI residue 34 LYS Chi-restraints excluded: chain TI residue 55 THR Chi-restraints excluded: chain TA residue 32 ARG Chi-restraints excluded: chain TA residue 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 116 LEU Chi-restraints excluded: chain TA residue 130 ILE Chi-restraints excluded: chain TA residue 135 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 164 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.0870 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** TD 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 31 GLN TD 42 ASN TD 80 GLN TE 31 GLN TE 42 ASN ** TF 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TF 31 GLN TF 80 GLN ** TH 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TH 31 GLN TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14754 Z= 0.360 Angle : 0.558 6.896 20094 Z= 0.306 Chirality : 0.046 0.156 2319 Planarity : 0.003 0.040 2685 Dihedral : 6.134 53.860 2067 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.20 % Allowed : 17.04 % 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: -0.21 (0.19), residues: 1884 helix: 2.18 (0.32), residues: 261 sheet: -0.05 (0.20), residues: 654 loop : -0.83 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPTA 65 HIS 0.005 0.001 HISTA 304 PHE 0.019 0.002 PHETB 354 TYR 0.025 0.002 TYRTB 290 ARG 0.009 0.001 ARGTI 95 *********************** 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 354 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 319 time to evaluate : 1.778 Fit side-chains REVERT: TC 7 ASP cc_start: 0.8561 (t0) cc_final: 0.8273 (t0) REVERT: TC 89 THR cc_start: 0.9294 (m) cc_final: 0.8974 (p) REVERT: TC 139 THR cc_start: 0.9637 (OUTLIER) cc_final: 0.9213 (t) REVERT: TD 83 GLN cc_start: 0.9076 (tt0) cc_final: 0.8776 (tt0) REVERT: TD 85 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8687 (mt-10) REVERT: TE 9 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8847 (tp40) REVERT: TE 92 THR cc_start: 0.9439 (m) cc_final: 0.9221 (p) REVERT: TF 58 ASP cc_start: 0.8756 (t0) cc_final: 0.8313 (t0) REVERT: TF 59 ASP cc_start: 0.9039 (m-30) cc_final: 0.8810 (t70) REVERT: TF 61 GLU cc_start: 0.8542 (mp0) cc_final: 0.8272 (mp0) REVERT: TF 85 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8520 (mt-10) REVERT: TF 112 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8385 (mt-10) REVERT: TG 58 ASP cc_start: 0.9046 (t70) cc_final: 0.8789 (t70) REVERT: TG 92 THR cc_start: 0.9508 (m) cc_final: 0.9226 (p) REVERT: TI 9 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8621 (tp-100) REVERT: TI 58 ASP cc_start: 0.8985 (t0) cc_final: 0.8569 (t0) REVERT: TI 59 ASP cc_start: 0.9050 (m-30) cc_final: 0.8805 (t0) REVERT: TI 92 THR cc_start: 0.9475 (m) cc_final: 0.9265 (p) REVERT: TA 89 THR cc_start: 0.9447 (m) cc_final: 0.9095 (p) REVERT: TB 164 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: TB 319 MET cc_start: 0.8948 (tmm) cc_final: 0.8690 (tmm) outliers start: 35 outliers final: 24 residues processed: 338 average time/residue: 1.1576 time to fit residues: 437.3914 Evaluate side-chains 341 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 313 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 40 ILE 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 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 26 LEU Chi-restraints excluded: chain TG residue 55 THR Chi-restraints excluded: chain TH residue 55 THR Chi-restraints excluded: chain TH residue 64 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 69 ILE Chi-restraints excluded: chain TA residue 95 VAL Chi-restraints excluded: chain TA residue 116 LEU Chi-restraints excluded: chain TA residue 135 VAL Chi-restraints excluded: chain TA residue 139 THR Chi-restraints excluded: chain TB residue 103 THR Chi-restraints excluded: chain TB residue 135 VAL Chi-restraints excluded: chain TB residue 139 THR Chi-restraints excluded: chain TB residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: TD 31 GLN 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 TH 83 GLN ** TI 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2942 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: