Starting phenix.real_space_refine on Thu Mar 5 02:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618.map" model { file = "/net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7una_26618/03_2026/7una_26618_trim.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 8 5.49 5 S 40 5.16 5 C 5918 2.51 5 N 1521 2.21 5 O 1724 1.98 5 H 9203 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18414 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2286 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain breaks: 4 Chain: "B" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2266 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "C" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2306 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 4 Chain: "D" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2298 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 3 Chain: "E" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2249 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 4 Chain: "F" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2277 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "G" Number of atoms: 2271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2271 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain breaks: 4 Chain: "H" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2281 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' 4BW A 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW A 401 " occ=0.47 residue: pdb=" C1' 4BW C 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW C 401 " occ=0.47 residue: pdb=" C1' 4BW F 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW F 401 " occ=0.47 residue: pdb=" C1' 4BW H 401 " occ=0.47 ... (43 atoms not shown) pdb=" PBS 4BW H 401 " occ=0.47 Time building chain proxies: 2.82, per 1000 atoms: 0.15 Number of scatterers: 18414 At special positions: 0 Unit cell: (134.2, 126.5, 171.6, 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 40 16.00 P 8 15.00 O 1724 8.00 N 1521 7.00 C 5918 6.00 H 9203 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 467.2 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 51.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 154 through 177 Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 262 through 273 removed outlier: 4.276A pdb=" N THR A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'B' and resid 154 through 177 Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 262 through 275 removed outlier: 4.293A pdb=" N THR B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 308 removed outlier: 3.658A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 177 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.964A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 308 removed outlier: 3.578A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 177 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.898A pdb=" N ILE D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 308 removed outlier: 3.540A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 177 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 262 through 275 removed outlier: 4.289A pdb=" N THR E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 308 removed outlier: 3.644A pdb=" N ASN E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 177 Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 262 through 274 removed outlier: 4.244A pdb=" N THR F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 308 Processing helix chain 'G' and resid 153 through 177 Processing helix chain 'G' and resid 206 through 218 Processing helix chain 'G' and resid 262 through 274 removed outlier: 4.234A pdb=" N THR G 266 " --> pdb=" O SER G 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 268 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 307 removed outlier: 3.861A pdb=" N ARG G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 177 Processing helix chain 'H' and resid 206 through 218 removed outlier: 3.593A pdb=" N TYR H 217 " --> pdb=" O TYR H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 275 removed outlier: 3.845A pdb=" N ILE H 267 " --> pdb=" O THR H 263 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 308 removed outlier: 3.640A pdb=" N ASN H 308 " --> pdb=" O LEU H 304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.032A pdb=" N ASN A 320 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA4, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.767A pdb=" N ASP B 259 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 196 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B 193 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU B 318 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 195 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA6, first strand: chain 'C' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'D' and resid 220 through 222 removed outlier: 4.099A pdb=" N HIS D 239 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 193 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 318 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 195 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN D 320 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE D 197 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AA9, first strand: chain 'E' and resid 257 through 259 removed outlier: 3.703A pdb=" N ASP E 259 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL E 193 " --> pdb=" O ASN E 316 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU E 318 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL E 195 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN E 320 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE E 197 " --> pdb=" O ASN E 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 220 through 222 Processing sheet with id=AB2, first strand: chain 'F' and resid 220 through 223 removed outlier: 3.594A pdb=" N HIS F 239 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL F 193 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 318 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 195 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN F 320 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 197 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 3.568A pdb=" N VAL G 179 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 193 through 198 removed outlier: 6.263A pdb=" N VAL G 193 " --> pdb=" O ASN G 316 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU G 318 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL G 195 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN G 320 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE G 197 " --> pdb=" O ASN G 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 220 through 222 removed outlier: 3.791A pdb=" N HIS H 239 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL H 193 " --> pdb=" O ASN H 316 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU H 318 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL H 195 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN H 320 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 197 " --> pdb=" O ASN H 320 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1431 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: 3.64 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9179 1.03 - 1.23: 27 1.23 - 1.42: 3844 1.42 - 1.61: 5454 1.61 - 1.81: 80 Bond restraints: 18584 Sorted by residual: bond pdb=" CBI 4BW A 401 " pdb=" CBM 4BW A 401 " ideal model delta sigma weight residual 1.538 1.289 0.249 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " ideal model delta sigma weight residual 1.538 1.290 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " ideal model delta sigma weight residual 1.538 1.291 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " ideal model delta sigma weight residual 1.538 1.293 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C4' 4BW C 401 " pdb=" O4' 4BW C 401 " ideal model delta sigma weight residual 1.445 1.656 -0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 18579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 33444 3.47 - 6.95: 81 6.95 - 10.42: 48 10.42 - 13.89: 8 13.89 - 17.36: 8 Bond angle restraints: 33589 Sorted by residual: angle pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 112.00 103.69 8.31 1.40e+00 5.10e-01 3.52e+01 angle pdb=" OAD 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sigma weight residual 122.13 104.77 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" OAD 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sigma weight residual 122.13 104.79 17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" OAD 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sigma weight residual 122.13 104.87 17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" OAD 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sigma weight residual 122.13 104.88 17.25 3.00e+00 1.11e-01 3.31e+01 ... (remaining 33584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 8525 32.68 - 65.36: 268 65.36 - 98.03: 16 98.03 - 130.71: 15 130.71 - 163.39: 13 Dihedral angle restraints: 8837 sinusoidal: 4926 harmonic: 3911 Sorted by residual: dihedral pdb=" CAN 4BW A 401 " pdb=" OAV 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sinusoidal sigma weight residual 330.18 166.79 163.39 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CAN 4BW H 401 " pdb=" OAV 4BW H 401 " pdb=" PBR 4BW H 401 " pdb=" OAH 4BW H 401 " ideal model delta sinusoidal sigma weight residual 330.18 167.73 162.45 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CAN 4BW F 401 " pdb=" OAV 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sinusoidal sigma weight residual 330.18 170.25 159.93 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1185 0.045 - 0.089: 187 0.089 - 0.134: 93 0.134 - 0.178: 15 0.178 - 0.223: 7 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CBI 4BW C 401 " pdb=" CBM 4BW C 401 " pdb=" CBO 4BW C 401 " pdb=" OAG 4BW C 401 " both_signs ideal model delta sigma weight residual False 2.67 2.45 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CBI 4BW H 401 " pdb=" CBM 4BW H 401 " pdb=" CBO 4BW H 401 " pdb=" OAG 4BW H 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CBI 4BW F 401 " pdb=" CBM 4BW F 401 " pdb=" CBO 4BW F 401 " pdb=" OAG 4BW F 401 " both_signs ideal model delta sigma weight residual False 2.67 2.47 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1484 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 236 " 0.077 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO A 237 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 163 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C ASN A 163 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 163 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 163 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN C 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 163 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 1167 2.20 - 2.80: 37925 2.80 - 3.40: 49727 3.40 - 4.00: 62165 4.00 - 4.60: 95811 Nonbonded interactions: 246795 Sorted by model distance: nonbonded pdb=" HG1 THR H 263 " pdb=" O3' 4BW H 401 " model vdw 1.594 2.450 nonbonded pdb=" O GLU F 172 " pdb=" HG SER F 176 " model vdw 1.596 2.450 nonbonded pdb=" OD1 ASN D 308 " pdb=" H ALA D 310 " model vdw 1.599 2.450 nonbonded pdb=" O GLU H 172 " pdb=" HG SER H 176 " model vdw 1.601 2.450 nonbonded pdb=" OD2 ASP G 194 " pdb=" HE2 HIS G 256 " model vdw 1.609 2.450 ... (remaining 246790 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 'A' and (resid 153 through 225 or (resid 235 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 236 through 241 or (resid 253 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name \ HG22 or name HG23)) or resid 254 through 274 or resid 285 through 321)) selection = (chain 'B' and (resid 153 through 184 or resid 186 through 225 or resid 235 thro \ ugh 241 or (resid 253 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 \ or name HG21 or name HG22 or name HG23)) or resid 254 through 274 or resid 285 \ through 321)) selection = (chain 'C' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or (resid 285 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 286 \ through 321)) selection = (chain 'D' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 321)) selection = (chain 'E' and (resid 153 through 225 or resid 235 through 241 or (resid 253 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 254 through 255 or (resid 256 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or \ name HE2)) or resid 257 through 274 or resid 285 through 321)) selection = (chain 'F' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 241 \ or (resid 253 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 254 through 274 or (resid 285 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name OD \ 2 or name HA or name HB2 or name HB3)) or resid 286 through 321)) selection = (chain 'G' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or resid 235 through 241 or (resid 253 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 through \ 255 or (resid 256 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 257 through 321)) \ selection = (chain 'H' and (resid 153 through 180 or (resid 185 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 186 through 225 \ or (resid 235 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 236 through 241 or (resid 253 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or na \ me HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 254 throu \ gh 274 or resid 285 through 321)) } 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=0.47 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.610 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: 0.070 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.610 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.015 0.848 9382 Z= 1.080 Angle : 1.018 17.363 12670 Z= 0.444 Chirality : 0.044 0.223 1487 Planarity : 0.006 0.111 1516 Dihedral : 18.090 163.389 3627 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 1054 helix: 0.94 (0.22), residues: 519 sheet: -2.23 (0.33), residues: 211 loop : -1.96 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 292 TYR 0.018 0.001 TYR F 162 PHE 0.019 0.001 PHE C 191 HIS 0.003 0.001 HIS F 174 Details of bonding type rmsd covalent geometry : bond 0.01271 ( 9381) covalent geometry : angle 1.01795 (12670) hydrogen bonds : bond 0.13246 ( 496) hydrogen bonds : angle 7.30052 ( 1431) Misc. bond : bond 0.84779 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASP cc_start: 0.7626 (m-30) cc_final: 0.7347 (m-30) REVERT: A 221 LYS cc_start: 0.6088 (pptt) cc_final: 0.5159 (pptt) REVERT: A 269 GLU cc_start: 0.7889 (mp0) cc_final: 0.7598 (mp0) REVERT: B 273 LEU cc_start: 0.8277 (mm) cc_final: 0.8064 (mm) REVERT: B 320 ASN cc_start: 0.7335 (t0) cc_final: 0.7036 (t0) REVERT: C 171 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8351 (mt-10) REVERT: C 172 GLU cc_start: 0.8089 (tt0) cc_final: 0.7822 (tt0) REVERT: D 172 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7712 (mp0) REVERT: D 292 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8214 (ttm-80) REVERT: F 159 ILE cc_start: 0.8183 (mt) cc_final: 0.7980 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1970 time to fit residues: 63.9192 Evaluate side-chains 180 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 214 ASN B 239 HIS B 316 ASN D 316 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.111439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098163 restraints weight = 67867.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101399 restraints weight = 32439.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103590 restraints weight = 19049.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104935 restraints weight = 12762.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.106021 restraints weight = 9585.252| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9382 Z= 0.216 Angle : 0.617 5.357 12670 Z= 0.334 Chirality : 0.044 0.197 1487 Planarity : 0.005 0.056 1516 Dihedral : 20.910 177.938 1449 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.26 % Allowed : 9.52 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1054 helix: 1.20 (0.22), residues: 523 sheet: -2.15 (0.34), residues: 211 loop : -1.66 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 292 TYR 0.022 0.002 TYR F 303 PHE 0.022 0.002 PHE C 191 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 9381) covalent geometry : angle 0.61726 (12670) hydrogen bonds : bond 0.04304 ( 496) hydrogen bonds : angle 6.05308 ( 1431) Misc. bond : bond 0.00385 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6389 (pptt) cc_final: 0.5425 (pptt) REVERT: A 269 GLU cc_start: 0.8298 (mp0) cc_final: 0.7753 (mp0) REVERT: B 292 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7386 (mmt90) REVERT: B 320 ASN cc_start: 0.7360 (t0) cc_final: 0.6889 (t0) REVERT: C 171 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 194 ASP cc_start: 0.8077 (t0) cc_final: 0.7875 (t0) REVERT: C 269 GLU cc_start: 0.8459 (mp0) cc_final: 0.8223 (mp0) REVERT: C 292 ARG cc_start: 0.7644 (mtp85) cc_final: 0.6848 (mmt-90) REVERT: D 290 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: E 291 MET cc_start: 0.7796 (tpt) cc_final: 0.7189 (tpp) REVERT: F 159 ILE cc_start: 0.8488 (mt) cc_final: 0.8244 (mt) REVERT: F 194 ASP cc_start: 0.7607 (m-30) cc_final: 0.7393 (t0) REVERT: G 286 MET cc_start: 0.7454 (mmp) cc_final: 0.7076 (mmp) outliers start: 23 outliers final: 17 residues processed: 197 average time/residue: 0.1847 time to fit residues: 51.5341 Evaluate side-chains 183 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 202 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN C 204 ASN D 316 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.104202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091713 restraints weight = 68363.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094686 restraints weight = 30033.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096754 restraints weight = 17120.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098065 restraints weight = 11372.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099063 restraints weight = 8451.565| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9382 Z= 0.182 Angle : 0.570 4.933 12670 Z= 0.310 Chirality : 0.042 0.242 1487 Planarity : 0.004 0.037 1516 Dihedral : 20.833 174.214 1449 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.16 % Allowed : 13.64 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 1054 helix: 1.42 (0.22), residues: 523 sheet: -2.18 (0.34), residues: 211 loop : -1.51 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 292 TYR 0.018 0.002 TYR F 303 PHE 0.014 0.002 PHE A 238 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9381) covalent geometry : angle 0.56995 (12670) hydrogen bonds : bond 0.04011 ( 496) hydrogen bonds : angle 5.81641 ( 1431) Misc. bond : bond 0.00444 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6677 (pptt) cc_final: 0.5752 (pptt) REVERT: A 269 GLU cc_start: 0.8242 (mp0) cc_final: 0.7668 (mp0) REVERT: B 320 ASN cc_start: 0.7049 (t0) cc_final: 0.6715 (t0) REVERT: C 171 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8214 (mt-10) REVERT: D 192 ARG cc_start: 0.8281 (pmt170) cc_final: 0.7989 (pmt-80) REVERT: D 290 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: E 291 MET cc_start: 0.7865 (tpt) cc_final: 0.7255 (tpp) REVERT: F 171 GLU cc_start: 0.7373 (tt0) cc_final: 0.7113 (tt0) outliers start: 22 outliers final: 16 residues processed: 190 average time/residue: 0.1795 time to fit residues: 48.8867 Evaluate side-chains 183 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 239 HIS C 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092233 restraints weight = 68619.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095220 restraints weight = 29778.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097307 restraints weight = 16872.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098552 restraints weight = 11131.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.099563 restraints weight = 8300.679| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9382 Z= 0.143 Angle : 0.534 5.752 12670 Z= 0.289 Chirality : 0.040 0.209 1487 Planarity : 0.004 0.037 1516 Dihedral : 20.858 175.893 1449 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.96 % Allowed : 14.23 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 1054 helix: 1.59 (0.22), residues: 523 sheet: -2.11 (0.34), residues: 224 loop : -1.24 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 292 TYR 0.020 0.001 TYR F 303 PHE 0.014 0.001 PHE G 240 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9381) covalent geometry : angle 0.53448 (12670) hydrogen bonds : bond 0.03654 ( 496) hydrogen bonds : angle 5.67746 ( 1431) Misc. bond : bond 0.00210 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6633 (pptt) cc_final: 0.5755 (pptt) REVERT: A 269 GLU cc_start: 0.8314 (mp0) cc_final: 0.7687 (mp0) REVERT: B 320 ASN cc_start: 0.7002 (t0) cc_final: 0.6610 (t0) REVERT: C 171 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 292 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6835 (mmt-90) REVERT: C 293 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: E 291 MET cc_start: 0.7794 (tpt) cc_final: 0.7239 (tpp) REVERT: F 171 GLU cc_start: 0.7376 (tt0) cc_final: 0.7156 (tt0) REVERT: F 194 ASP cc_start: 0.7732 (m-30) cc_final: 0.7485 (t0) REVERT: F 303 TYR cc_start: 0.7689 (t80) cc_final: 0.7192 (t80) REVERT: G 191 PHE cc_start: 0.8074 (t80) cc_final: 0.7564 (t80) REVERT: H 254 ASP cc_start: 0.7778 (m-30) cc_final: 0.7548 (m-30) outliers start: 20 outliers final: 15 residues processed: 183 average time/residue: 0.1738 time to fit residues: 45.2467 Evaluate side-chains 180 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.103620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091114 restraints weight = 68225.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094119 restraints weight = 30199.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096160 restraints weight = 17316.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097417 restraints weight = 11498.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098368 restraints weight = 8618.417| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9382 Z= 0.159 Angle : 0.543 5.834 12670 Z= 0.293 Chirality : 0.041 0.226 1487 Planarity : 0.004 0.044 1516 Dihedral : 20.879 177.368 1449 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.65 % Allowed : 15.31 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.27), residues: 1054 helix: 1.65 (0.22), residues: 522 sheet: -2.04 (0.34), residues: 224 loop : -1.14 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 292 TYR 0.022 0.001 TYR F 303 PHE 0.012 0.001 PHE F 297 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9381) covalent geometry : angle 0.54282 (12670) hydrogen bonds : bond 0.03646 ( 496) hydrogen bonds : angle 5.58361 ( 1431) Misc. bond : bond 0.00230 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6690 (pptt) cc_final: 0.5832 (pptt) REVERT: A 269 GLU cc_start: 0.8384 (mp0) cc_final: 0.7800 (mp0) REVERT: B 307 ARG cc_start: 0.7366 (ttp80) cc_final: 0.6894 (ttm-80) REVERT: B 320 ASN cc_start: 0.6990 (t0) cc_final: 0.6561 (t0) REVERT: C 194 ASP cc_start: 0.8153 (t0) cc_final: 0.7945 (t0) REVERT: C 291 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7691 (ptm) REVERT: C 293 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: D 290 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: E 291 MET cc_start: 0.7782 (tpt) cc_final: 0.7270 (tpp) REVERT: F 168 ARG cc_start: 0.8309 (mmm160) cc_final: 0.7830 (mmm160) REVERT: F 171 GLU cc_start: 0.7390 (tt0) cc_final: 0.6833 (tt0) REVERT: G 191 PHE cc_start: 0.8081 (t80) cc_final: 0.7622 (t80) REVERT: H 254 ASP cc_start: 0.7811 (m-30) cc_final: 0.7604 (m-30) outliers start: 27 outliers final: 19 residues processed: 193 average time/residue: 0.1934 time to fit residues: 52.8333 Evaluate side-chains 192 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 166 ILE Chi-restraints excluded: chain H residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.104396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092007 restraints weight = 67450.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.095028 restraints weight = 29364.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097034 restraints weight = 16668.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098317 restraints weight = 11016.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099285 restraints weight = 8204.838| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9382 Z= 0.126 Angle : 0.522 6.122 12670 Z= 0.280 Chirality : 0.040 0.202 1487 Planarity : 0.004 0.038 1516 Dihedral : 20.857 176.728 1449 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.06 % Allowed : 16.58 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1054 helix: 1.80 (0.21), residues: 523 sheet: -2.01 (0.35), residues: 216 loop : -0.93 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 292 TYR 0.025 0.001 TYR F 303 PHE 0.011 0.001 PHE A 238 HIS 0.004 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9381) covalent geometry : angle 0.52174 (12670) hydrogen bonds : bond 0.03381 ( 496) hydrogen bonds : angle 5.50166 ( 1431) Misc. bond : bond 0.00196 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6687 (pptt) cc_final: 0.5850 (pptt) REVERT: A 269 GLU cc_start: 0.8476 (mp0) cc_final: 0.7833 (mp0) REVERT: B 307 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6850 (ttm-80) REVERT: B 320 ASN cc_start: 0.6811 (t0) cc_final: 0.6355 (t0) REVERT: C 194 ASP cc_start: 0.8135 (t0) cc_final: 0.7899 (t0) REVERT: C 292 ARG cc_start: 0.7412 (mmt-90) cc_final: 0.6943 (ttm-80) REVERT: C 293 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5628 (mp0) REVERT: D 290 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: E 291 MET cc_start: 0.7727 (tpt) cc_final: 0.7286 (tpp) REVERT: F 168 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7804 (mmm160) REVERT: F 171 GLU cc_start: 0.7412 (tt0) cc_final: 0.6868 (tt0) REVERT: F 269 GLU cc_start: 0.7640 (mp0) cc_final: 0.7385 (mp0) REVERT: G 191 PHE cc_start: 0.8081 (t80) cc_final: 0.7610 (t80) REVERT: G 286 MET cc_start: 0.7567 (mmp) cc_final: 0.7311 (mmp) REVERT: H 254 ASP cc_start: 0.7843 (m-30) cc_final: 0.7630 (m-30) outliers start: 21 outliers final: 16 residues processed: 189 average time/residue: 0.1900 time to fit residues: 50.5304 Evaluate side-chains 186 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS C 204 ASN D 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.104043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091624 restraints weight = 67890.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094664 restraints weight = 29522.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096659 restraints weight = 16657.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097931 restraints weight = 11067.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098926 restraints weight = 8296.948| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9382 Z= 0.132 Angle : 0.525 6.127 12670 Z= 0.282 Chirality : 0.040 0.204 1487 Planarity : 0.004 0.040 1516 Dihedral : 20.844 176.530 1449 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.55 % Allowed : 17.76 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.27), residues: 1054 helix: 1.86 (0.21), residues: 523 sheet: -1.85 (0.35), residues: 216 loop : -0.84 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 292 TYR 0.017 0.001 TYR F 162 PHE 0.014 0.001 PHE A 191 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9381) covalent geometry : angle 0.52532 (12670) hydrogen bonds : bond 0.03373 ( 496) hydrogen bonds : angle 5.44837 ( 1431) Misc. bond : bond 0.00202 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6689 (pptt) cc_final: 0.5861 (pptt) REVERT: A 269 GLU cc_start: 0.8510 (mp0) cc_final: 0.7838 (mp0) REVERT: B 307 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6857 (ttm-80) REVERT: B 320 ASN cc_start: 0.6798 (t0) cc_final: 0.6329 (t0) REVERT: C 194 ASP cc_start: 0.8091 (t0) cc_final: 0.7863 (t0) REVERT: C 291 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7725 (ptt) REVERT: C 293 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: D 290 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: E 291 MET cc_start: 0.7770 (tpt) cc_final: 0.7369 (tpp) REVERT: F 168 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7864 (mmm160) REVERT: F 171 GLU cc_start: 0.7444 (tt0) cc_final: 0.6917 (tt0) REVERT: F 269 GLU cc_start: 0.7696 (mp0) cc_final: 0.7426 (mp0) REVERT: F 301 LEU cc_start: 0.8431 (tp) cc_final: 0.8002 (mp) REVERT: G 191 PHE cc_start: 0.8077 (t80) cc_final: 0.7677 (t80) REVERT: G 286 MET cc_start: 0.7608 (mmp) cc_final: 0.7325 (mmp) REVERT: H 254 ASP cc_start: 0.7859 (m-30) cc_final: 0.7636 (m-30) outliers start: 26 outliers final: 16 residues processed: 186 average time/residue: 0.2013 time to fit residues: 51.4130 Evaluate side-chains 190 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN D 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.105515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093007 restraints weight = 67340.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096095 restraints weight = 29365.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098192 restraints weight = 16644.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099450 restraints weight = 10982.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100485 restraints weight = 8191.177| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9382 Z= 0.109 Angle : 0.510 6.091 12670 Z= 0.271 Chirality : 0.040 0.186 1487 Planarity : 0.004 0.046 1516 Dihedral : 20.874 178.304 1449 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.06 % Allowed : 18.16 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.27), residues: 1054 helix: 2.00 (0.21), residues: 521 sheet: -1.85 (0.35), residues: 213 loop : -0.64 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 292 TYR 0.016 0.001 TYR F 162 PHE 0.011 0.001 PHE A 191 HIS 0.003 0.000 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9381) covalent geometry : angle 0.50982 (12670) hydrogen bonds : bond 0.03135 ( 496) hydrogen bonds : angle 5.35626 ( 1431) Misc. bond : bond 0.00171 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6679 (pptt) cc_final: 0.5866 (pptt) REVERT: A 269 GLU cc_start: 0.8518 (mp0) cc_final: 0.7806 (mp0) REVERT: B 307 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6844 (ttm-80) REVERT: B 320 ASN cc_start: 0.6754 (t0) cc_final: 0.6262 (t0) REVERT: C 194 ASP cc_start: 0.8091 (t0) cc_final: 0.7840 (t0) REVERT: C 289 LEU cc_start: 0.6973 (tp) cc_final: 0.6426 (tp) REVERT: C 291 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7769 (ptt) REVERT: C 293 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5528 (mp0) REVERT: C 303 TYR cc_start: 0.8487 (t80) cc_final: 0.8152 (t80) REVERT: D 290 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: E 177 GLU cc_start: 0.7338 (pm20) cc_final: 0.6918 (mt-10) REVERT: E 291 MET cc_start: 0.7727 (tpt) cc_final: 0.7341 (tpp) REVERT: F 168 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7855 (mmm160) REVERT: F 171 GLU cc_start: 0.7357 (tt0) cc_final: 0.6858 (tt0) REVERT: F 269 GLU cc_start: 0.7738 (mp0) cc_final: 0.7505 (mp0) REVERT: F 301 LEU cc_start: 0.8399 (tp) cc_final: 0.8041 (mp) REVERT: G 191 PHE cc_start: 0.8054 (t80) cc_final: 0.7655 (t80) REVERT: G 286 MET cc_start: 0.7644 (mmp) cc_final: 0.7390 (mmp) outliers start: 21 outliers final: 14 residues processed: 186 average time/residue: 0.2084 time to fit residues: 53.6580 Evaluate side-chains 187 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN D 316 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.103721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090867 restraints weight = 68203.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094026 restraints weight = 29225.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096132 restraints weight = 16420.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097574 restraints weight = 10827.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.098540 restraints weight = 7856.692| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9382 Z= 0.164 Angle : 0.547 5.941 12670 Z= 0.294 Chirality : 0.041 0.213 1487 Planarity : 0.004 0.046 1516 Dihedral : 20.835 176.767 1449 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.26 % Allowed : 18.65 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1054 helix: 1.94 (0.22), residues: 523 sheet: -1.79 (0.35), residues: 214 loop : -0.75 (0.39), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 292 TYR 0.027 0.001 TYR F 162 PHE 0.014 0.001 PHE A 191 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9381) covalent geometry : angle 0.54673 (12670) hydrogen bonds : bond 0.03407 ( 496) hydrogen bonds : angle 5.38522 ( 1431) Misc. bond : bond 0.00225 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6689 (pptt) cc_final: 0.5873 (pptt) REVERT: A 269 GLU cc_start: 0.8569 (mp0) cc_final: 0.7818 (mp0) REVERT: B 307 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6938 (ttm-80) REVERT: B 320 ASN cc_start: 0.6860 (t0) cc_final: 0.6386 (t0) REVERT: C 194 ASP cc_start: 0.8082 (t0) cc_final: 0.7851 (t0) REVERT: C 289 LEU cc_start: 0.7082 (tp) cc_final: 0.6486 (tp) REVERT: C 291 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7783 (ptt) REVERT: C 293 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5544 (mp0) REVERT: C 303 TYR cc_start: 0.8519 (t80) cc_final: 0.8200 (t80) REVERT: E 177 GLU cc_start: 0.7359 (pm20) cc_final: 0.6921 (mt-10) REVERT: E 291 MET cc_start: 0.7844 (tpt) cc_final: 0.7316 (tpp) REVERT: F 168 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7853 (mmm160) REVERT: F 171 GLU cc_start: 0.7415 (tt0) cc_final: 0.6873 (tt0) REVERT: F 269 GLU cc_start: 0.7623 (mp0) cc_final: 0.7323 (mp0) REVERT: F 301 LEU cc_start: 0.8491 (tp) cc_final: 0.8038 (mp) REVERT: G 191 PHE cc_start: 0.8104 (t80) cc_final: 0.7788 (t80) REVERT: G 286 MET cc_start: 0.7677 (mmp) cc_final: 0.7380 (mmp) outliers start: 23 outliers final: 17 residues processed: 185 average time/residue: 0.1991 time to fit residues: 51.0071 Evaluate side-chains 189 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 ASN D 316 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.091880 restraints weight = 67776.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095015 restraints weight = 29257.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097087 restraints weight = 16489.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098471 restraints weight = 10891.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.099430 restraints weight = 7935.166| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9382 Z= 0.118 Angle : 0.520 6.907 12670 Z= 0.276 Chirality : 0.040 0.195 1487 Planarity : 0.004 0.044 1516 Dihedral : 20.847 178.721 1449 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.16 % Allowed : 18.94 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1054 helix: 2.04 (0.21), residues: 522 sheet: -1.86 (0.35), residues: 211 loop : -0.58 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 292 TYR 0.030 0.001 TYR F 162 PHE 0.011 0.001 PHE A 238 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9381) covalent geometry : angle 0.52003 (12670) hydrogen bonds : bond 0.03230 ( 496) hydrogen bonds : angle 5.35300 ( 1431) Misc. bond : bond 0.00187 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.6710 (pptt) cc_final: 0.5886 (pptt) REVERT: A 269 GLU cc_start: 0.8559 (mp0) cc_final: 0.7682 (mp0) REVERT: B 307 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6930 (ttm-80) REVERT: B 320 ASN cc_start: 0.6807 (t0) cc_final: 0.6308 (t0) REVERT: C 194 ASP cc_start: 0.8062 (t0) cc_final: 0.7802 (t0) REVERT: C 291 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7684 (ptt) REVERT: C 303 TYR cc_start: 0.8479 (t80) cc_final: 0.8154 (t80) REVERT: D 290 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: E 177 GLU cc_start: 0.7330 (pm20) cc_final: 0.6796 (mt-10) REVERT: E 291 MET cc_start: 0.7742 (tpt) cc_final: 0.7251 (tpp) REVERT: F 168 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7854 (mmm160) REVERT: F 171 GLU cc_start: 0.7370 (tt0) cc_final: 0.6861 (tt0) REVERT: F 269 GLU cc_start: 0.7715 (mp0) cc_final: 0.7455 (mp0) REVERT: F 301 LEU cc_start: 0.8477 (tp) cc_final: 0.8016 (mp) REVERT: G 191 PHE cc_start: 0.8046 (t80) cc_final: 0.7661 (t80) REVERT: G 286 MET cc_start: 0.7678 (mmp) cc_final: 0.7396 (mmp) outliers start: 22 outliers final: 19 residues processed: 182 average time/residue: 0.2091 time to fit residues: 52.3782 Evaluate side-chains 187 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain H residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS C 204 ASN ** F 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092101 restraints weight = 67384.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095293 restraints weight = 28328.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097373 restraints weight = 15729.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.098739 restraints weight = 10309.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099719 restraints weight = 7522.920| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9382 Z= 0.120 Angle : 0.522 6.698 12670 Z= 0.278 Chirality : 0.040 0.192 1487 Planarity : 0.004 0.045 1516 Dihedral : 20.858 178.904 1449 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.16 % Allowed : 19.23 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 1054 helix: 2.09 (0.21), residues: 521 sheet: -1.85 (0.36), residues: 211 loop : -0.57 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 292 TYR 0.027 0.001 TYR F 162 PHE 0.011 0.001 PHE A 238 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9381) covalent geometry : angle 0.52191 (12670) hydrogen bonds : bond 0.03203 ( 496) hydrogen bonds : angle 5.33370 ( 1431) Misc. bond : bond 0.00186 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.58 seconds wall clock time: 49 minutes 26.66 seconds (2966.66 seconds total)