Starting phenix.real_space_refine on Wed Feb 4 06:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966.map" model { file = "/net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixa_60966/02_2026/9ixa_60966_neut.cif" } resolution = 3.11 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= 0.046 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5588 2.51 5 N 1532 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8909 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2678 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 26, 'TRANS': 312} Chain: "B" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2915 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 358} Chain: "H" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1671 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1631 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8909 At special positions: 0 Unit cell: (92.4, 117.48, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1733 8.00 N 1532 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 28 " distance=2.02 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 266 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 225 " distance=2.05 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 220 " distance=2.02 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.14 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.12 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 263 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 246.9 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 23 sheets defined 7.0% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.617A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 196 through 200 Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38 removed outlier: 6.965A pdb=" N GLN A 49 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 37 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 47 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N SER A 51 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N MET A 70 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS A 66 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 86 removed outlier: 4.061A pdb=" N GLU A 109 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 156 Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 4.256A pdb=" N THR A 196 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 278 Processing sheet with id=AA9, first strand: chain 'A' and resid 307 through 311 Processing sheet with id=AB1, first strand: chain 'B' and resid 1 through 8 Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 19 removed outlier: 6.642A pdb=" N LYS B 132 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 48 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B 118 " --> pdb=" O THR B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 147 current: chain 'B' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 186 current: chain 'B' and resid 213 through 215 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 213 through 215 current: chain 'B' and resid 267 through 269 Processing sheet with id=AB3, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 101 through 110 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB5, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'B' and resid 297 through 305 removed outlier: 5.346A pdb=" N ASP B 298 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 324 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 346 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY B 326 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE B 344 " --> pdb=" O GLY B 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 343 through 356 current: chain 'B' and resid 372 through 379 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 111 through 114 Processing sheet with id=AB9, first strand: chain 'H' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 147 through 156 current: chain 'H' and resid 187 through 195 Processing sheet with id=AC1, first strand: chain 'H' and resid 161 through 165 removed outlier: 4.471A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 98 through 99 Processing sheet with id=AC4, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.020A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.262A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 564 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: 1.24 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2541 1.33 - 1.46: 1848 1.46 - 1.58: 4663 1.58 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 9128 Sorted by residual: bond pdb=" CA PRO L 120 " pdb=" C PRO L 120 " ideal model delta sigma weight residual 1.514 1.529 -0.015 5.50e-03 3.31e+04 7.51e+00 bond pdb=" NE ARG B 134 " pdb=" CZ ARG B 134 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.10e-02 8.26e+03 6.71e+00 bond pdb=" NE ARG B 267 " pdb=" CZ ARG B 267 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.55e+00 bond pdb=" C5 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.413 1.461 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" CG ASP H 112 " pdb=" OD1 ASP H 112 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.67e+00 ... (remaining 9123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10834 1.60 - 3.20: 1266 3.20 - 4.80: 177 4.80 - 6.40: 88 6.40 - 8.00: 58 Bond angle restraints: 12423 Sorted by residual: angle pdb=" C PHE L 119 " pdb=" N PRO L 120 " pdb=" CA PRO L 120 " ideal model delta sigma weight residual 119.66 126.67 -7.01 7.30e-01 1.88e+00 9.22e+01 angle pdb=" C TYR B 189 " pdb=" N PRO B 190 " pdb=" CA PRO B 190 " ideal model delta sigma weight residual 119.66 126.15 -6.49 7.20e-01 1.93e+00 8.12e+01 angle pdb=" C PRO A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 120.03 127.96 -7.93 9.90e-01 1.02e+00 6.41e+01 angle pdb=" C GLY H 129 " pdb=" N PRO H 130 " pdb=" CA PRO H 130 " ideal model delta sigma weight residual 119.85 127.85 -8.00 1.01e+00 9.80e-01 6.28e+01 angle pdb=" C ALA B 255 " pdb=" N PRO B 256 " pdb=" CA PRO B 256 " ideal model delta sigma weight residual 120.21 127.81 -7.60 9.60e-01 1.09e+00 6.26e+01 ... (remaining 12418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5321 17.88 - 35.77: 139 35.77 - 53.65: 47 53.65 - 71.53: 17 71.53 - 89.41: 9 Dihedral angle restraints: 5533 sinusoidal: 2175 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS B 68 " pdb=" SG CYS B 68 " pdb=" SG CYS B 78 " pdb=" CB CYS B 78 " ideal model delta sinusoidal sigma weight residual 93.00 163.66 -70.66 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.28 43.72 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 207 " pdb=" CB CYS H 207 " ideal model delta sinusoidal sigma weight residual 93.00 54.88 38.12 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 5530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 981 0.055 - 0.110: 322 0.110 - 0.165: 72 0.165 - 0.220: 7 0.220 - 0.275: 3 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CA TYR L 141 " pdb=" N TYR L 141 " pdb=" C TYR L 141 " pdb=" CB TYR L 141 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2 NAG A 401 " pdb=" C1 NAG A 401 " pdb=" C3 NAG A 401 " pdb=" N2 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.77 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE H 157 " pdb=" N PHE H 157 " pdb=" C PHE H 157 " pdb=" CB PHE H 157 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1382 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 122 " 0.023 2.00e-02 2.50e+03 1.17e-02 2.75e+00 pdb=" CG TYR B 122 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 122 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 122 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 122 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 122 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 122 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 95 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C TYR H 95 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR H 95 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS H 96 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 122 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C TYR B 122 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR B 122 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 123 " -0.009 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3255 2.88 - 3.38: 7619 3.38 - 3.89: 15343 3.89 - 4.39: 16953 4.39 - 4.90: 29245 Nonbonded interactions: 72415 Sorted by model distance: nonbonded pdb=" ND1 HIS H 211 " pdb=" OG SER H 214 " model vdw 2.370 3.120 nonbonded pdb=" OG1 THR A 211 " pdb=" O THR A 213 " model vdw 2.374 3.040 nonbonded pdb=" O THR L 94 " pdb=" NH1 ARG L 97 " model vdw 2.433 3.120 nonbonded pdb=" OE1 GLU A 40 " pdb=" OH TYR A 156 " model vdw 2.436 3.040 nonbonded pdb=" NZ LYS B 325 " pdb=" OE2 GLU B 345 " model vdw 2.461 3.120 ... (remaining 72410 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.020 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.010 0.107 9147 Z= 0.562 Angle : 1.267 10.817 12462 Z= 0.875 Chirality : 0.056 0.275 1385 Planarity : 0.004 0.017 1610 Dihedral : 10.377 89.412 3327 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.10 % Allowed : 0.70 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.11 (0.24), residues: 1150 helix: -2.17 (0.80), residues: 29 sheet: 1.82 (0.23), residues: 475 loop : 1.43 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.023 0.003 TYR B 122 PHE 0.019 0.002 PHE H 157 TRP 0.016 0.003 TRP B 170 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.01010 ( 9128) covalent geometry : angle 1.23638 (12423) SS BOND : bond 0.03459 ( 18) SS BOND : angle 5.30599 ( 36) hydrogen bonds : bond 0.16756 ( 238) hydrogen bonds : angle 9.30324 ( 564) link_NAG-ASN : bond 0.05041 ( 1) link_NAG-ASN : angle 1.99311 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.6855 (m-70) cc_final: 0.6542 (m-70) REVERT: A 264 VAL cc_start: 0.8423 (m) cc_final: 0.8142 (p) REVERT: A 285 MET cc_start: 0.7093 (mtm) cc_final: 0.6621 (mtp) REVERT: A 305 ASN cc_start: 0.8373 (t0) cc_final: 0.8049 (t0) REVERT: A 337 LYS cc_start: 0.7007 (mttt) cc_final: 0.6795 (mmtm) REVERT: B 48 THR cc_start: 0.7527 (m) cc_final: 0.7321 (m) REVERT: B 333 MET cc_start: 0.2647 (mmp) cc_final: 0.2180 (mmp) REVERT: H 73 ASP cc_start: 0.8410 (t0) cc_final: 0.8123 (t0) REVERT: H 100 MET cc_start: 0.8987 (mtp) cc_final: 0.8384 (mtp) REVERT: H 138 SER cc_start: 0.5436 (m) cc_final: 0.5044 (t) REVERT: L 148 GLN cc_start: 0.7896 (mt0) cc_final: 0.7669 (mt0) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1246 time to fit residues: 30.8137 Evaluate side-chains 105 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN H 84 ASN L 34 ASN L 125 GLN L 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.201424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156433 restraints weight = 10421.012| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.49 r_work: 0.3425 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9147 Z= 0.142 Angle : 0.582 8.270 12462 Z= 0.312 Chirality : 0.045 0.178 1385 Planarity : 0.005 0.048 1610 Dihedral : 4.409 16.575 1270 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.31 % Allowed : 5.14 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.70 (0.24), residues: 1150 helix: -1.44 (0.91), residues: 29 sheet: 1.62 (0.22), residues: 489 loop : 0.98 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 267 TYR 0.018 0.001 TYR B 122 PHE 0.016 0.001 PHE H 157 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9128) covalent geometry : angle 0.57780 (12423) SS BOND : bond 0.00425 ( 18) SS BOND : angle 1.39773 ( 36) hydrogen bonds : bond 0.04377 ( 238) hydrogen bonds : angle 6.87196 ( 564) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 0.96440 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7283 (m-70) cc_final: 0.6930 (m-70) REVERT: A 285 MET cc_start: 0.7187 (mtm) cc_final: 0.6711 (mtp) REVERT: A 305 ASN cc_start: 0.8419 (t0) cc_final: 0.8111 (t0) REVERT: B 48 THR cc_start: 0.7698 (m) cc_final: 0.7399 (m) REVERT: B 67 GLU cc_start: 0.7517 (tt0) cc_final: 0.7062 (mp0) REVERT: B 245 LYS cc_start: 0.8066 (mttt) cc_final: 0.7834 (mptt) REVERT: B 333 MET cc_start: 0.2024 (mmp) cc_final: 0.1660 (mmp) REVERT: H 30 ASP cc_start: 0.7627 (t0) cc_final: 0.7422 (t0) REVERT: H 100 MET cc_start: 0.8847 (mtp) cc_final: 0.7990 (mtp) REVERT: L 70 ASP cc_start: 0.7932 (m-30) cc_final: 0.7596 (p0) REVERT: L 148 GLN cc_start: 0.8098 (mt0) cc_final: 0.7669 (mt0) outliers start: 13 outliers final: 8 residues processed: 127 average time/residue: 0.1004 time to fit residues: 17.1780 Evaluate side-chains 110 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 0.0070 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN H 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.196271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154785 restraints weight = 10411.874| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.56 r_work: 0.3377 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9147 Z= 0.158 Angle : 0.564 10.014 12462 Z= 0.295 Chirality : 0.046 0.174 1385 Planarity : 0.004 0.045 1610 Dihedral : 4.366 21.011 1270 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 6.55 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.45 (0.25), residues: 1150 helix: -0.83 (0.97), residues: 29 sheet: 1.51 (0.23), residues: 493 loop : 0.72 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 221 TYR 0.018 0.002 TYR B 122 PHE 0.017 0.001 PHE H 157 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9128) covalent geometry : angle 0.55738 (12423) SS BOND : bond 0.00496 ( 18) SS BOND : angle 1.71303 ( 36) hydrogen bonds : bond 0.03637 ( 238) hydrogen bonds : angle 6.35519 ( 564) link_NAG-ASN : bond 0.00500 ( 1) link_NAG-ASN : angle 0.83150 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7575 (m-70) cc_final: 0.7204 (m-70) REVERT: A 117 ASP cc_start: 0.8600 (p0) cc_final: 0.8375 (p0) REVERT: A 285 MET cc_start: 0.7272 (mtm) cc_final: 0.6818 (mtp) REVERT: A 305 ASN cc_start: 0.8525 (t0) cc_final: 0.8303 (t0) REVERT: B 39 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7069 (mt-10) REVERT: B 48 THR cc_start: 0.7928 (m) cc_final: 0.7632 (m) REVERT: B 67 GLU cc_start: 0.7736 (tt0) cc_final: 0.7261 (mp0) REVERT: B 245 LYS cc_start: 0.8295 (mttt) cc_final: 0.8020 (mptt) REVERT: B 333 MET cc_start: 0.1866 (mmp) cc_final: 0.1483 (mmp) REVERT: H 25 SER cc_start: 0.8635 (p) cc_final: 0.8270 (m) REVERT: H 30 ASP cc_start: 0.7536 (t0) cc_final: 0.7130 (t0) REVERT: H 100 MET cc_start: 0.8878 (mtp) cc_final: 0.8112 (mtp) REVERT: L 70 ASP cc_start: 0.8197 (m-30) cc_final: 0.7788 (p0) REVERT: L 148 GLN cc_start: 0.8173 (mt0) cc_final: 0.7825 (mt0) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.0982 time to fit residues: 15.9248 Evaluate side-chains 116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 85 optimal weight: 0.0040 chunk 105 optimal weight: 0.0170 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155392 restraints weight = 10493.225| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.82 r_work: 0.3367 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9147 Z= 0.105 Angle : 0.514 10.862 12462 Z= 0.266 Chirality : 0.044 0.161 1385 Planarity : 0.004 0.048 1610 Dihedral : 4.197 18.020 1270 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.61 % Allowed : 8.36 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.41 (0.25), residues: 1150 helix: -0.61 (0.98), residues: 30 sheet: 1.49 (0.22), residues: 503 loop : 0.65 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 221 TYR 0.014 0.001 TYR L 193 PHE 0.010 0.001 PHE H 157 TRP 0.008 0.001 TRP B 243 HIS 0.003 0.001 HIS H 211 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9128) covalent geometry : angle 0.50940 (12423) SS BOND : bond 0.00233 ( 18) SS BOND : angle 1.41857 ( 36) hydrogen bonds : bond 0.03116 ( 238) hydrogen bonds : angle 6.00998 ( 564) link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 0.73976 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 HIS cc_start: 0.7547 (m-70) cc_final: 0.7233 (m-70) REVERT: A 117 ASP cc_start: 0.8486 (p0) cc_final: 0.8252 (p0) REVERT: A 285 MET cc_start: 0.7550 (mtm) cc_final: 0.7154 (mtp) REVERT: B 48 THR cc_start: 0.7761 (m) cc_final: 0.7468 (m) REVERT: B 67 GLU cc_start: 0.7466 (tt0) cc_final: 0.7130 (mp0) REVERT: B 333 MET cc_start: 0.1972 (mmp) cc_final: 0.1533 (mmp) REVERT: H 25 SER cc_start: 0.8550 (p) cc_final: 0.8198 (m) REVERT: H 30 ASP cc_start: 0.7204 (t0) cc_final: 0.6793 (t0) REVERT: H 100 MET cc_start: 0.8782 (mtp) cc_final: 0.8035 (mtp) REVERT: H 171 THR cc_start: 0.8202 (t) cc_final: 0.7925 (m) REVERT: L 70 ASP cc_start: 0.8073 (m-30) cc_final: 0.7726 (p0) REVERT: L 148 GLN cc_start: 0.8022 (mt0) cc_final: 0.7747 (mt0) outliers start: 16 outliers final: 13 residues processed: 118 average time/residue: 0.1113 time to fit residues: 17.4074 Evaluate side-chains 120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 chunk 102 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.195220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.153454 restraints weight = 10401.746| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.81 r_work: 0.3343 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9147 Z= 0.143 Angle : 0.539 10.283 12462 Z= 0.276 Chirality : 0.045 0.148 1385 Planarity : 0.004 0.045 1610 Dihedral : 4.215 20.713 1270 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.57 % Rotamer: Outliers : 2.01 % Allowed : 8.46 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.23 (0.25), residues: 1150 helix: -0.73 (0.94), residues: 31 sheet: 1.46 (0.23), residues: 489 loop : 0.46 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 221 TYR 0.015 0.001 TYR L 141 PHE 0.015 0.001 PHE H 157 TRP 0.010 0.001 TRP B 243 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9128) covalent geometry : angle 0.53322 (12423) SS BOND : bond 0.00224 ( 18) SS BOND : angle 1.50180 ( 36) hydrogen bonds : bond 0.03066 ( 238) hydrogen bonds : angle 5.91078 ( 564) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 0.91714 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8795 (tttt) cc_final: 0.8440 (tttt) REVERT: A 117 ASP cc_start: 0.8711 (p0) cc_final: 0.8481 (p0) REVERT: A 202 ASN cc_start: 0.8084 (m-40) cc_final: 0.7708 (m-40) REVERT: A 285 MET cc_start: 0.7586 (mtm) cc_final: 0.7223 (mtp) REVERT: B 48 THR cc_start: 0.7923 (m) cc_final: 0.7609 (m) REVERT: B 67 GLU cc_start: 0.7784 (tt0) cc_final: 0.7242 (mp0) REVERT: B 333 MET cc_start: 0.1856 (mmp) cc_final: 0.1457 (mmp) REVERT: H 25 SER cc_start: 0.8643 (p) cc_final: 0.8282 (m) REVERT: H 30 ASP cc_start: 0.7616 (t0) cc_final: 0.7203 (t0) REVERT: H 100 MET cc_start: 0.8971 (mtp) cc_final: 0.8171 (mtp) REVERT: H 171 THR cc_start: 0.8284 (t) cc_final: 0.8007 (m) REVERT: L 70 ASP cc_start: 0.8267 (m-30) cc_final: 0.7785 (p0) REVERT: L 148 GLN cc_start: 0.8296 (mt0) cc_final: 0.7594 (mm-40) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.1220 time to fit residues: 18.8235 Evaluate side-chains 121 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 332 ASN L 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.194084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153079 restraints weight = 10415.492| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.37 r_work: 0.3323 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9147 Z= 0.146 Angle : 0.540 10.123 12462 Z= 0.276 Chirality : 0.045 0.143 1385 Planarity : 0.004 0.047 1610 Dihedral : 4.252 19.721 1270 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 2.11 % Allowed : 8.26 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.07 (0.25), residues: 1150 helix: -0.81 (0.92), residues: 31 sheet: 1.41 (0.23), residues: 491 loop : 0.29 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 221 TYR 0.017 0.001 TYR L 141 PHE 0.015 0.001 PHE H 157 TRP 0.007 0.001 TRP B 243 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9128) covalent geometry : angle 0.53538 (12423) SS BOND : bond 0.00243 ( 18) SS BOND : angle 1.43137 ( 36) hydrogen bonds : bond 0.02965 ( 238) hydrogen bonds : angle 5.82791 ( 564) link_NAG-ASN : bond 0.00123 ( 1) link_NAG-ASN : angle 1.02010 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8774 (tttt) cc_final: 0.8476 (tttt) REVERT: A 117 ASP cc_start: 0.8745 (p0) cc_final: 0.8504 (p0) REVERT: A 285 MET cc_start: 0.7623 (mtm) cc_final: 0.7262 (mtp) REVERT: B 67 GLU cc_start: 0.7887 (tt0) cc_final: 0.7277 (mp0) REVERT: B 333 MET cc_start: 0.1607 (mmp) cc_final: 0.1257 (mmp) REVERT: H 25 SER cc_start: 0.8695 (p) cc_final: 0.8312 (m) REVERT: H 30 ASP cc_start: 0.7644 (t0) cc_final: 0.7211 (t0) REVERT: H 100 MET cc_start: 0.8995 (mtp) cc_final: 0.8585 (mtp) REVERT: H 171 THR cc_start: 0.8386 (t) cc_final: 0.8100 (m) REVERT: L 70 ASP cc_start: 0.8289 (m-30) cc_final: 0.7771 (p0) REVERT: L 148 GLN cc_start: 0.8407 (mt0) cc_final: 0.7661 (mm110) outliers start: 21 outliers final: 13 residues processed: 118 average time/residue: 0.1260 time to fit residues: 19.5500 Evaluate side-chains 116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.0070 chunk 30 optimal weight: 0.3980 chunk 69 optimal weight: 0.0370 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 332 ASN B 175 ASN L 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.196394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155091 restraints weight = 10434.700| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.96 r_work: 0.3356 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9147 Z= 0.089 Angle : 0.497 10.476 12462 Z= 0.254 Chirality : 0.044 0.145 1385 Planarity : 0.004 0.047 1610 Dihedral : 4.049 19.937 1270 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 1.41 % Allowed : 9.37 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.14 (0.26), residues: 1150 helix: -0.66 (0.93), residues: 31 sheet: 1.41 (0.23), residues: 502 loop : 0.35 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 143 TYR 0.015 0.001 TYR L 141 PHE 0.011 0.001 PHE H 157 TRP 0.007 0.001 TRP B 243 HIS 0.002 0.000 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 9128) covalent geometry : angle 0.49273 (12423) SS BOND : bond 0.00172 ( 18) SS BOND : angle 1.32386 ( 36) hydrogen bonds : bond 0.02753 ( 238) hydrogen bonds : angle 5.55566 ( 564) link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 0.89420 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8760 (tttt) cc_final: 0.8517 (tttt) REVERT: A 117 ASP cc_start: 0.8714 (p0) cc_final: 0.8488 (p0) REVERT: A 285 MET cc_start: 0.7542 (mtm) cc_final: 0.7201 (mtp) REVERT: A 337 LYS cc_start: 0.7712 (mttt) cc_final: 0.7408 (mmtt) REVERT: B 67 GLU cc_start: 0.7928 (tt0) cc_final: 0.7233 (mp0) REVERT: B 333 MET cc_start: 0.1665 (mmp) cc_final: 0.1294 (mmp) REVERT: H 25 SER cc_start: 0.8625 (p) cc_final: 0.8272 (m) REVERT: H 30 ASP cc_start: 0.7397 (t0) cc_final: 0.6973 (t0) REVERT: H 100 MET cc_start: 0.8987 (mtp) cc_final: 0.8258 (mtp) REVERT: H 171 THR cc_start: 0.8463 (t) cc_final: 0.8182 (m) REVERT: L 18 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7896 (ttt90) REVERT: L 70 ASP cc_start: 0.8283 (m-30) cc_final: 0.7780 (p0) REVERT: L 148 GLN cc_start: 0.8283 (mt0) cc_final: 0.7705 (mm-40) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.1032 time to fit residues: 15.3312 Evaluate side-chains 116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.0060 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN L 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.193119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151736 restraints weight = 10368.580| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 4.37 r_work: 0.3301 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9147 Z= 0.167 Angle : 0.553 10.273 12462 Z= 0.282 Chirality : 0.046 0.143 1385 Planarity : 0.004 0.044 1610 Dihedral : 4.238 21.027 1270 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 1.71 % Allowed : 9.87 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.01 (0.26), residues: 1150 helix: -0.79 (0.91), residues: 31 sheet: 1.43 (0.23), residues: 489 loop : 0.19 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 221 TYR 0.016 0.002 TYR L 141 PHE 0.018 0.001 PHE H 157 TRP 0.010 0.001 TRP B 243 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9128) covalent geometry : angle 0.54731 (12423) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.50976 ( 36) hydrogen bonds : bond 0.02944 ( 238) hydrogen bonds : angle 5.70854 ( 564) link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 1.29470 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8772 (tttt) cc_final: 0.8504 (tttt) REVERT: A 117 ASP cc_start: 0.8878 (p0) cc_final: 0.8606 (p0) REVERT: A 285 MET cc_start: 0.7653 (mtm) cc_final: 0.7278 (mtp) REVERT: B 67 GLU cc_start: 0.7868 (tt0) cc_final: 0.7255 (mp0) REVERT: B 333 MET cc_start: 0.1753 (mmp) cc_final: 0.1450 (mmp) REVERT: H 30 ASP cc_start: 0.7642 (t0) cc_final: 0.7201 (t0) REVERT: H 100 MET cc_start: 0.9020 (mtp) cc_final: 0.8668 (mtp) REVERT: H 171 THR cc_start: 0.8466 (t) cc_final: 0.8238 (m) REVERT: L 70 ASP cc_start: 0.8333 (m-30) cc_final: 0.7795 (p0) REVERT: L 148 GLN cc_start: 0.8329 (mt0) cc_final: 0.7719 (mm-40) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 0.1102 time to fit residues: 16.1396 Evaluate side-chains 112 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 98 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.194778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154723 restraints weight = 10274.251| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 4.33 r_work: 0.3325 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9147 Z= 0.116 Angle : 0.518 10.291 12462 Z= 0.263 Chirality : 0.045 0.148 1385 Planarity : 0.004 0.045 1610 Dihedral : 4.133 20.927 1270 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 1.31 % Allowed : 9.97 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.01 (0.26), residues: 1150 helix: -0.66 (0.94), residues: 31 sheet: 1.38 (0.23), residues: 495 loop : 0.21 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 119 TYR 0.016 0.001 TYR L 141 PHE 0.014 0.001 PHE H 157 TRP 0.008 0.001 TRP B 243 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9128) covalent geometry : angle 0.51369 (12423) SS BOND : bond 0.00221 ( 18) SS BOND : angle 1.37075 ( 36) hydrogen bonds : bond 0.02754 ( 238) hydrogen bonds : angle 5.59826 ( 564) link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 1.03873 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8751 (tttt) cc_final: 0.8512 (tttt) REVERT: A 117 ASP cc_start: 0.8829 (p0) cc_final: 0.8562 (p0) REVERT: A 150 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7530 (tt0) REVERT: A 285 MET cc_start: 0.7632 (mtm) cc_final: 0.7267 (mtp) REVERT: B 67 GLU cc_start: 0.7849 (tt0) cc_final: 0.7248 (mp0) REVERT: B 333 MET cc_start: 0.1739 (mmp) cc_final: 0.1455 (mmp) REVERT: H 25 SER cc_start: 0.8663 (p) cc_final: 0.8313 (m) REVERT: H 30 ASP cc_start: 0.7504 (t0) cc_final: 0.6831 (p0) REVERT: H 100 MET cc_start: 0.8992 (mtp) cc_final: 0.8620 (mtp) REVERT: H 171 THR cc_start: 0.8511 (t) cc_final: 0.8270 (m) REVERT: H 221 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7251 (ttp80) REVERT: L 18 ARG cc_start: 0.8117 (ttt90) cc_final: 0.7812 (ttt90) REVERT: L 70 ASP cc_start: 0.8320 (m-30) cc_final: 0.7802 (p0) REVERT: L 148 GLN cc_start: 0.8322 (mt0) cc_final: 0.7731 (mm-40) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.1095 time to fit residues: 16.8855 Evaluate side-chains 108 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 224 GLN A 232 HIS L 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140448 restraints weight = 10393.010| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.61 r_work: 0.3426 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9147 Z= 0.170 Angle : 0.565 10.098 12462 Z= 0.287 Chirality : 0.046 0.142 1385 Planarity : 0.004 0.043 1610 Dihedral : 4.281 22.087 1270 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.41 % Allowed : 10.07 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.84 (0.26), residues: 1150 helix: -0.75 (0.93), residues: 31 sheet: 1.25 (0.23), residues: 495 loop : 0.11 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 119 TYR 0.017 0.002 TYR L 141 PHE 0.019 0.001 PHE H 157 TRP 0.010 0.001 TRP B 243 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9128) covalent geometry : angle 0.55970 (12423) SS BOND : bond 0.00327 ( 18) SS BOND : angle 1.46123 ( 36) hydrogen bonds : bond 0.02883 ( 238) hydrogen bonds : angle 5.69117 ( 564) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.41295 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8667 (p0) cc_final: 0.8337 (p0) REVERT: A 150 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7122 (tt0) REVERT: A 285 MET cc_start: 0.7739 (mtm) cc_final: 0.7425 (mtp) REVERT: A 287 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5985 (mt) REVERT: B 333 MET cc_start: 0.2073 (mmp) cc_final: 0.1663 (mmp) REVERT: H 30 ASP cc_start: 0.7402 (t0) cc_final: 0.6858 (p0) REVERT: H 171 THR cc_start: 0.8465 (t) cc_final: 0.8255 (m) REVERT: L 18 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7652 (ttt90) REVERT: L 70 ASP cc_start: 0.8135 (m-30) cc_final: 0.7777 (p0) REVERT: L 148 GLN cc_start: 0.8184 (mt0) cc_final: 0.7809 (mm-40) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.1201 time to fit residues: 17.2453 Evaluate side-chains 113 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 71 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.193428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147006 restraints weight = 10288.185| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.42 r_work: 0.3423 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9147 Z= 0.146 Angle : 0.543 9.859 12462 Z= 0.276 Chirality : 0.045 0.145 1385 Planarity : 0.004 0.043 1610 Dihedral : 4.255 22.232 1270 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.96 % Favored : 96.96 % Rotamer: Outliers : 1.21 % Allowed : 10.67 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.26), residues: 1150 helix: -0.75 (0.94), residues: 31 sheet: 1.19 (0.23), residues: 504 loop : 0.11 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 119 TYR 0.017 0.001 TYR L 141 PHE 0.016 0.001 PHE H 157 TRP 0.008 0.001 TRP B 243 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9128) covalent geometry : angle 0.53725 (12423) SS BOND : bond 0.00311 ( 18) SS BOND : angle 1.48017 ( 36) hydrogen bonds : bond 0.02831 ( 238) hydrogen bonds : angle 5.63305 ( 564) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.28750 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3132.12 seconds wall clock time: 54 minutes 8.00 seconds (3248.00 seconds total)