Starting phenix.real_space_refine on Wed Feb 14 12:46:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d14_27115/02_2024/8d14_27115_updated.pdb" } resolution = 2.51 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= 0.003 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 5541 2.51 5 N 1482 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9225 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Time building chain proxies: 5.50, per 1000 atoms: 0.60 Number of scatterers: 9225 At special positions: 0 Unit cell: (89.61, 85.49, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 9 15.00 Mg 3 11.99 O 2127 8.00 N 1482 7.00 C 5541 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 - 3.50 Amino acid : False - 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: 4.11 Conformation dependent library (CDL) restraints added in 1.5 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 43.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.920A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.721A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 5.600A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.981A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.767A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.921A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.721A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 5.601A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.981A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.766A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.921A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.721A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 5.599A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.983A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.765A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.889A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.887A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.406A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.888A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 318 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1599 1.32 - 1.45: 2228 1.45 - 1.57: 5041 1.57 - 1.69: 9 1.69 - 1.81: 111 Bond restraints: 8988 Sorted by residual: bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" O3 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O2 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 100.06 - 107.34: 401 107.34 - 114.62: 5297 114.62 - 121.90: 4604 121.90 - 129.18: 1842 129.18 - 136.47: 57 Bond angle restraints: 12201 Sorted by residual: angle pdb=" N GLN B 137 " pdb=" CA GLN B 137 " pdb=" C GLN B 137 " ideal model delta sigma weight residual 111.33 118.60 -7.27 1.21e+00 6.83e-01 3.61e+01 angle pdb=" N GLN A 137 " pdb=" CA GLN A 137 " pdb=" C GLN A 137 " ideal model delta sigma weight residual 111.33 117.10 -5.77 1.21e+00 6.83e-01 2.27e+01 angle pdb=" N GLN C 137 " pdb=" CA GLN C 137 " pdb=" C GLN C 137 " ideal model delta sigma weight residual 111.33 116.50 -5.17 1.21e+00 6.83e-01 1.82e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.71 110.56 3.15 9.50e-01 1.11e+00 1.10e+01 ... (remaining 12196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 5268 30.90 - 61.79: 108 61.79 - 92.69: 12 92.69 - 123.59: 3 123.59 - 154.49: 6 Dihedral angle restraints: 5397 sinusoidal: 2181 harmonic: 3216 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 94.49 -154.49 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 90.10 -150.10 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.60 -149.60 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1210 0.073 - 0.147: 136 0.147 - 0.220: 4 0.220 - 0.294: 0 0.294 - 0.367: 3 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA GLN B 137 " pdb=" N GLN B 137 " pdb=" C GLN B 137 " pdb=" CB GLN B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA GLN A 137 " pdb=" N GLN A 137 " pdb=" C GLN A 137 " pdb=" CB GLN A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA GLN C 137 " pdb=" N GLN C 137 " pdb=" C GLN C 137 " pdb=" CB GLN C 137 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1350 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 134 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C VAL C 134 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 134 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 135 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 134 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C VAL A 134 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL A 134 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 135 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 321 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 322 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.018 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 247 2.63 - 3.20: 8301 3.20 - 3.77: 16005 3.77 - 4.33: 23095 4.33 - 4.90: 34855 Nonbonded interactions: 82503 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O HOH C 546 " model vdw 2.064 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 548 " model vdw 2.066 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 587 " model vdw 2.067 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 562 " model vdw 2.067 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 594 " model vdw 2.068 2.170 ... (remaining 82498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 6.820 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: 0.000 Extract box with map and model: 29.030 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.090 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.004 0.061 8988 Z= 0.242 Angle : 0.572 8.716 12201 Z= 0.296 Chirality : 0.046 0.367 1353 Planarity : 0.003 0.033 1557 Dihedral : 13.460 154.485 3339 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.32 % Allowed : 3.83 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.26), residues: 1098 helix: 0.82 (0.26), residues: 459 sheet: 0.38 (0.34), residues: 207 loop : 1.79 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 340 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.160 Fit side-chains REVERT: A 82 MET cc_start: 0.9046 (tpt) cc_final: 0.8730 (tpt) REVERT: B 305 MET cc_start: 0.8353 (mmm) cc_final: 0.8017 (mmm) REVERT: C 44 MET cc_start: 0.8146 (mtp) cc_final: 0.7730 (mtp) REVERT: C 82 MET cc_start: 0.8974 (tpt) cc_final: 0.8650 (tpt) REVERT: C 227 MET cc_start: 0.8453 (mmm) cc_final: 0.8164 (mmm) REVERT: C 364 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6276 (mm-30) outliers start: 3 outliers final: 0 residues processed: 109 average time/residue: 1.8847 time to fit residues: 215.3053 Evaluate side-chains 68 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 360 GLN B 353 GLN C 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8988 Z= 0.239 Angle : 0.578 6.890 12201 Z= 0.282 Chirality : 0.047 0.150 1353 Planarity : 0.005 0.032 1557 Dihedral : 11.608 166.520 1251 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.49 % Allowed : 8.20 % Favored : 90.31 % 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: 1.51 (0.27), residues: 1098 helix: 0.65 (0.25), residues: 462 sheet: 0.49 (0.35), residues: 207 loop : 2.08 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.006 0.002 HIS C 371 PHE 0.012 0.002 PHE C 255 TYR 0.009 0.001 TYR B 143 ARG 0.008 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9097 (tpt) cc_final: 0.8873 (tpt) REVERT: B 305 MET cc_start: 0.8329 (mmm) cc_final: 0.8076 (mmm) REVERT: B 355 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7286 (mmm) REVERT: C 82 MET cc_start: 0.8987 (tpt) cc_final: 0.8750 (tpt) REVERT: C 227 MET cc_start: 0.8549 (mmm) cc_final: 0.8231 (mmm) REVERT: C 355 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7234 (mtp) outliers start: 14 outliers final: 5 residues processed: 75 average time/residue: 2.0097 time to fit residues: 158.1059 Evaluate side-chains 69 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.210 Angle : 0.551 6.740 12201 Z= 0.265 Chirality : 0.046 0.148 1353 Planarity : 0.004 0.037 1557 Dihedral : 11.634 171.366 1251 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.17 % Allowed : 8.63 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1098 helix: 0.44 (0.25), residues: 462 sheet: 0.47 (0.35), residues: 207 loop : 2.06 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.010 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8845 (pp) REVERT: A 82 MET cc_start: 0.9069 (tpt) cc_final: 0.8832 (tpt) REVERT: B 123 MET cc_start: 0.8874 (mmp) cc_final: 0.8663 (tpt) REVERT: B 305 MET cc_start: 0.8310 (mmm) cc_final: 0.8034 (mmm) REVERT: B 355 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: C 82 MET cc_start: 0.8989 (tpt) cc_final: 0.8734 (tpt) REVERT: C 227 MET cc_start: 0.8601 (mmm) cc_final: 0.8270 (mmm) REVERT: C 241 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: C 355 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7113 (mtp) outliers start: 11 outliers final: 4 residues processed: 72 average time/residue: 1.8967 time to fit residues: 143.8485 Evaluate side-chains 71 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8988 Z= 0.243 Angle : 0.565 7.021 12201 Z= 0.272 Chirality : 0.047 0.153 1353 Planarity : 0.004 0.030 1557 Dihedral : 11.688 172.655 1251 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.38 % Allowed : 8.84 % Favored : 89.78 % 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: 1.27 (0.26), residues: 1098 helix: 0.36 (0.25), residues: 462 sheet: 0.47 (0.36), residues: 207 loop : 2.00 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.002 PHE C 255 TYR 0.009 0.001 TYR C 143 ARG 0.006 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 82 MET cc_start: 0.9081 (tpt) cc_final: 0.8808 (tpt) REVERT: B 305 MET cc_start: 0.8312 (mmm) cc_final: 0.8053 (mmm) REVERT: B 355 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: C 47 MET cc_start: 0.6411 (ppp) cc_final: 0.6179 (ppp) REVERT: C 82 MET cc_start: 0.8993 (tpt) cc_final: 0.8698 (tpt) REVERT: C 227 MET cc_start: 0.8602 (mmm) cc_final: 0.8269 (mmm) REVERT: C 241 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: C 353 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8154 (mp-120) REVERT: C 355 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7087 (mtp) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 1.8038 time to fit residues: 139.2027 Evaluate side-chains 75 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.208 Angle : 0.547 6.877 12201 Z= 0.261 Chirality : 0.045 0.152 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.665 173.765 1251 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.17 % Allowed : 9.58 % Favored : 89.24 % 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: 1.25 (0.26), residues: 1098 helix: 0.35 (0.25), residues: 462 sheet: 0.45 (0.36), residues: 207 loop : 1.98 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 82 MET cc_start: 0.9070 (tpt) cc_final: 0.8826 (tpt) REVERT: B 305 MET cc_start: 0.8305 (mmm) cc_final: 0.8040 (mmm) REVERT: B 355 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7241 (mtm) REVERT: C 227 MET cc_start: 0.8615 (mmm) cc_final: 0.8288 (mmm) REVERT: C 241 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 355 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7102 (mtp) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 1.8012 time to fit residues: 133.0555 Evaluate side-chains 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8988 Z= 0.259 Angle : 0.573 7.130 12201 Z= 0.276 Chirality : 0.047 0.158 1353 Planarity : 0.004 0.031 1557 Dihedral : 11.725 173.444 1251 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.70 % Allowed : 9.37 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1098 helix: 0.31 (0.25), residues: 459 sheet: 0.28 (0.36), residues: 213 loop : 1.99 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.002 PHE A 31 TYR 0.009 0.001 TYR C 143 ARG 0.004 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 305 MET cc_start: 0.8305 (mmm) cc_final: 0.8051 (mmm) REVERT: B 355 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7226 (mtm) REVERT: C 227 MET cc_start: 0.8632 (mmm) cc_final: 0.8303 (mmm) REVERT: C 241 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: C 355 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7069 (mtp) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 1.7320 time to fit residues: 135.5552 Evaluate side-chains 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.0000 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.186 Angle : 0.541 6.777 12201 Z= 0.257 Chirality : 0.045 0.149 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.657 175.668 1251 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.70 % Allowed : 9.90 % Favored : 88.39 % 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: 1.23 (0.27), residues: 1098 helix: 0.34 (0.25), residues: 462 sheet: 0.38 (0.36), residues: 207 loop : 2.00 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8833 (pp) REVERT: A 314 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7983 (tp40) REVERT: B 113 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8228 (mtpp) REVERT: B 305 MET cc_start: 0.8311 (mmm) cc_final: 0.8055 (mmm) REVERT: B 355 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7218 (mtm) REVERT: C 227 MET cc_start: 0.8618 (mmm) cc_final: 0.8275 (mmm) REVERT: C 241 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: C 355 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7054 (mtp) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 1.7394 time to fit residues: 135.8859 Evaluate side-chains 74 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.167 Angle : 0.537 6.609 12201 Z= 0.253 Chirality : 0.044 0.146 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.640 179.294 1251 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.38 % Allowed : 10.44 % Favored : 88.18 % 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: 1.28 (0.27), residues: 1098 helix: 0.39 (0.25), residues: 462 sheet: 0.36 (0.36), residues: 207 loop : 2.05 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8859 (pp) REVERT: A 314 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7995 (tp40) REVERT: B 113 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8221 (mtpp) REVERT: B 305 MET cc_start: 0.8311 (mmm) cc_final: 0.8055 (mmm) REVERT: B 355 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7231 (mtm) REVERT: C 227 MET cc_start: 0.8609 (mmm) cc_final: 0.8267 (mmm) REVERT: C 241 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: C 355 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7046 (mtp) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 1.7122 time to fit residues: 130.2462 Evaluate side-chains 72 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0470 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8988 Z= 0.142 Angle : 0.530 7.851 12201 Z= 0.247 Chirality : 0.043 0.144 1353 Planarity : 0.004 0.033 1557 Dihedral : 11.427 169.194 1251 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.60 % Allowed : 10.33 % Favored : 88.07 % 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: 1.37 (0.27), residues: 1098 helix: 0.44 (0.25), residues: 462 sheet: 0.40 (0.36), residues: 207 loop : 2.12 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.007 0.001 TYR C 143 ARG 0.004 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8854 (pp) REVERT: A 314 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7998 (tp40) REVERT: B 113 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: B 305 MET cc_start: 0.8335 (mmm) cc_final: 0.8085 (mmm) REVERT: B 355 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7257 (mtm) REVERT: C 227 MET cc_start: 0.8577 (mmm) cc_final: 0.8230 (mmm) REVERT: C 241 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: C 355 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7052 (mtp) outliers start: 15 outliers final: 6 residues processed: 73 average time/residue: 1.7863 time to fit residues: 138.2819 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8988 Z= 0.157 Angle : 0.540 7.754 12201 Z= 0.252 Chirality : 0.044 0.147 1353 Planarity : 0.004 0.032 1557 Dihedral : 11.362 169.280 1251 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.49 % Allowed : 10.54 % Favored : 87.97 % 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: 1.38 (0.27), residues: 1098 helix: 0.43 (0.25), residues: 462 sheet: 0.45 (0.36), residues: 207 loop : 2.13 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 79 HIS 0.003 0.001 HIS B 161 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG C 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 64 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8829 (pp) REVERT: A 314 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: B 113 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: B 305 MET cc_start: 0.8312 (mmm) cc_final: 0.8057 (mmm) REVERT: B 355 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7249 (mtm) REVERT: C 227 MET cc_start: 0.8569 (mmm) cc_final: 0.8219 (mmm) REVERT: C 241 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: C 355 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7050 (mtp) outliers start: 14 outliers final: 6 residues processed: 71 average time/residue: 1.8383 time to fit residues: 137.5996 Evaluate side-chains 73 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.070733 restraints weight = 13282.789| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.52 r_work: 0.2788 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8988 Z= 0.303 Angle : 0.605 7.860 12201 Z= 0.290 Chirality : 0.048 0.163 1353 Planarity : 0.004 0.030 1557 Dihedral : 11.758 178.224 1251 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.38 % Allowed : 10.76 % Favored : 87.86 % 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: 1.14 (0.27), residues: 1098 helix: 0.27 (0.25), residues: 459 sheet: 0.27 (0.36), residues: 213 loop : 1.99 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 340 HIS 0.005 0.002 HIS B 161 PHE 0.010 0.002 PHE A 31 TYR 0.011 0.001 TYR C 143 ARG 0.004 0.001 ARG C 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.36 seconds wall clock time: 63 minutes 47.15 seconds (3827.15 seconds total)