Starting phenix.real_space_refine on Mon May 4 09:22:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377.map" model { file = "/net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qub_53377/05_2026/9qub_53377_trim.cif" } resolution = 2.7 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= 0.004 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 2 5.49 5 S 66 5.16 5 C 8348 2.51 5 N 2074 2.21 5 O 2389 1.98 5 H 7044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19923 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1380 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 171} Chain breaks: 2 Chain: "E" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1639 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1639 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6828 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain: "A" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6828 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19923 At special positions: 0 Unit cell: (94.608, 116.64, 139.32, 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 66 16.00 P 2 15.00 O 2389 8.00 N 2074 7.00 C 8348 6.00 H 7044 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=1.92 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 853.2 milliseconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 21 sheets defined 49.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.719A pdb=" N ILE C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.670A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.661A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.521A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 196 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.514A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.708A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 removed outlier: 4.241A pdb=" N SER F 169 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 196 Processing helix chain 'B' and resid 82 through 106 Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 113 through 135 Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.888A pdb=" N GLY B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.622A pdb=" N ASN B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 192 Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.536A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 226 Proline residue: B 211 - end of helix removed outlier: 3.655A pdb=" N TYR B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 245 through 259 Proline residue: B 251 - end of helix Processing helix chain 'B' and resid 266 through 276 removed outlier: 4.020A pdb=" N SER B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 Processing helix chain 'B' and resid 298 through 325 removed outlier: 3.859A pdb=" N GLY B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 358 Processing helix chain 'B' and resid 361 through 378 removed outlier: 3.602A pdb=" N LEU B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 407 Proline residue: B 398 - end of helix Processing helix chain 'B' and resid 417 through 440 removed outlier: 3.553A pdb=" N VAL B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.765A pdb=" N ALA B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 Processing helix chain 'B' and resid 481 through 517 Proline residue: B 503 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'A' and resid 82 through 106 Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 113 through 135 Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.889A pdb=" N GLY A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.623A pdb=" N ASN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.537A pdb=" N LYS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 Proline residue: A 211 - end of helix removed outlier: 3.655A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 245 through 259 Proline residue: A 251 - end of helix Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.021A pdb=" N SER A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 4.165A pdb=" N LEU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.858A pdb=" N GLY A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 358 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.602A pdb=" N LEU A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 407 Proline residue: A 398 - end of helix Processing helix chain 'A' and resid 417 through 440 removed outlier: 3.553A pdb=" N VAL A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.766A pdb=" N ALA A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 481 through 517 Proline residue: A 503 - end of helix Proline residue: A 514 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.536A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 116 through 118 removed outlier: 5.702A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.543A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.543A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.513A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.513A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 116 through 118 removed outlier: 5.787A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER E 174 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.578A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.561A pdb=" N THR D 161 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS D 207 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 173 through 177 removed outlier: 5.254A pdb=" N SER D 186 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 177 " --> pdb=" O THR D 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.721A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AC2, first strand: chain 'F' and resid 173 through 177 removed outlier: 4.219A pdb=" N SER F 186 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA F 176 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR F 184 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 205 through 207 removed outlier: 4.117A pdb=" N HIS F 207 " --> pdb=" O THR F 212 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2067 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: 5.08 Time building geometry restraints manager: 2.91 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: 7024 1.03 - 1.23: 39 1.23 - 1.42: 5344 1.42 - 1.62: 7710 1.62 - 1.81: 94 Bond restraints: 20211 Sorted by residual: bond pdb=" O5 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 2.278 1.678 0.600 2.00e-02 2.50e+03 9.01e+02 bond pdb=" O5 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 2.278 1.678 0.600 2.00e-02 2.50e+03 8.99e+02 bond pdb=" O4 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 1.764 1.505 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" O4 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 1.764 1.505 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C6 LPP A 601 " pdb=" O5 LPP A 601 " ideal model delta sigma weight residual 1.243 1.425 -0.182 2.00e-02 2.50e+03 8.29e+01 ... (remaining 20206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.28: 33871 9.28 - 18.55: 10 18.55 - 27.83: 2 27.83 - 37.10: 4 37.10 - 46.38: 2 Bond angle restraints: 33889 Sorted by residual: angle pdb=" O4 LPP A 601 " pdb=" P1 LPP A 601 " pdb=" O5 LPP A 601 " ideal model delta sigma weight residual 62.99 109.37 -46.38 3.00e+00 1.11e-01 2.39e+02 angle pdb=" O4 LPP B 601 " pdb=" P1 LPP B 601 " pdb=" O5 LPP B 601 " ideal model delta sigma weight residual 62.99 109.34 -46.35 3.00e+00 1.11e-01 2.39e+02 angle pdb=" C6 LPP B 601 " pdb=" O5 LPP B 601 " pdb=" P1 LPP B 601 " ideal model delta sigma weight residual 82.33 118.66 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C6 LPP A 601 " pdb=" O5 LPP A 601 " pdb=" P1 LPP A 601 " ideal model delta sigma weight residual 82.33 118.65 -36.32 3.00e+00 1.11e-01 1.47e+02 angle pdb=" O2 LPP A 601 " pdb=" P1 LPP A 601 " pdb=" O3 LPP A 601 " ideal model delta sigma weight residual 142.11 109.48 32.63 3.00e+00 1.11e-01 1.18e+02 ... (remaining 33884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8897 17.68 - 35.37: 943 35.37 - 53.05: 319 53.05 - 70.74: 81 70.74 - 88.42: 17 Dihedral angle restraints: 10257 sinusoidal: 5041 harmonic: 5216 Sorted by residual: dihedral pdb=" CB CYS D 148 " pdb=" SG CYS D 148 " pdb=" SG CYS D 203 " pdb=" CB CYS D 203 " ideal model delta sinusoidal sigma weight residual 93.00 150.08 -57.08 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS E 134 " pdb=" SG CYS E 134 " pdb=" SG CYS E 194 " pdb=" CB CYS E 194 " ideal model delta sinusoidal sigma weight residual -86.00 -142.80 56.80 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS F 148 " pdb=" SG CYS F 148 " pdb=" SG CYS F 203 " pdb=" CB CYS F 203 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 ... (remaining 10254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2077 0.115 - 0.230: 30 0.230 - 0.346: 0 0.346 - 0.461: 0 0.461 - 0.576: 1 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA LYS C 142 " pdb=" N LYS C 142 " pdb=" C LYS C 142 " pdb=" CB LYS C 142 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.30e+00 chirality pdb=" CA PRO C 141 " pdb=" N PRO C 141 " pdb=" C PRO C 141 " pdb=" CB PRO C 141 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA SER C 65 " pdb=" N SER C 65 " pdb=" C SER C 65 " pdb=" CB SER C 65 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2105 not shown) Planarity restraints: 3049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 281 " -0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" N ALA B 282 " 0.060 2.00e-02 2.50e+03 pdb=" CA ALA B 282 " -0.015 2.00e-02 2.50e+03 pdb=" H ALA B 282 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 280 " 0.014 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" N LEU A 281 " -0.045 2.00e-02 2.50e+03 pdb=" CA LEU A 281 " 0.011 2.00e-02 2.50e+03 pdb=" H LEU A 281 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 156 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO F 157 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 157 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 157 " 0.028 5.00e-02 4.00e+02 ... (remaining 3046 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1623 2.24 - 2.83: 33786 2.83 - 3.42: 44476 3.42 - 4.01: 61677 4.01 - 4.60: 95847 Nonbonded interactions: 237409 Sorted by model distance: nonbonded pdb="HD13 LEU B 438 " pdb=" HG CYS B 441 " model vdw 1.654 2.440 nonbonded pdb=" O GLY A 405 " pdb="HG22 VAL A 408 " model vdw 1.880 2.620 nonbonded pdb=" O GLY B 405 " pdb="HG22 VAL B 408 " model vdw 1.881 2.620 nonbonded pdb=" H VAL A 408 " pdb="HG22 VAL A 408 " model vdw 1.886 2.270 nonbonded pdb=" H VAL B 408 " pdb="HG22 VAL B 408 " model vdw 1.887 2.270 ... (remaining 237404 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 151 or resid 159 through 179 or resid 190 throug \ h 196)) } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 0.600 13175 Z= 0.480 Angle : 1.021 46.377 17911 Z= 0.446 Chirality : 0.043 0.576 2108 Planarity : 0.003 0.051 2203 Dihedral : 16.016 88.423 4705 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.42 % Allowed : 25.30 % Favored : 74.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.56 % 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: 0.73 (0.22), residues: 1665 helix: 2.33 (0.20), residues: 733 sheet: -0.27 (0.31), residues: 323 loop : -1.46 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.017 0.001 TYR F 183 PHE 0.026 0.001 PHE A 327 TRP 0.012 0.001 TRP D 196 HIS 0.003 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00954 (13167) covalent geometry : angle 1.01971 (17895) SS BOND : bond 0.03862 ( 8) SS BOND : angle 2.16638 ( 16) hydrogen bonds : bond 0.14613 ( 719) hydrogen bonds : angle 6.56976 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.8944 (tt) cc_final: 0.8680 (tm) REVERT: C 175 MET cc_start: 0.8778 (tpp) cc_final: 0.8465 (tpt) REVERT: E 107 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8722 (ttmm) REVERT: E 123 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8228 (tm-30) REVERT: E 155 ARG cc_start: 0.8514 (ptm160) cc_final: 0.7673 (ptm160) REVERT: D 73 ASP cc_start: 0.8912 (t0) cc_final: 0.8642 (t0) REVERT: D 82 GLU cc_start: 0.8775 (tp30) cc_final: 0.8546 (tp30) REVERT: F 73 ASP cc_start: 0.8734 (t0) cc_final: 0.8429 (t0) outliers start: 6 outliers final: 2 residues processed: 139 average time/residue: 0.8191 time to fit residues: 126.0599 Evaluate side-chains 125 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain D residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063793 restraints weight = 65171.891| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.34 r_work: 0.2823 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13175 Z= 0.171 Angle : 0.538 6.318 17911 Z= 0.282 Chirality : 0.039 0.155 2108 Planarity : 0.003 0.049 2203 Dihedral : 6.844 55.775 1868 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.81 % Allowed : 23.54 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.70 (0.22), residues: 1665 helix: 2.21 (0.19), residues: 744 sheet: -0.27 (0.32), residues: 310 loop : -1.38 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.013 0.001 TYR F 183 PHE 0.021 0.001 PHE A 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00381 (13167) covalent geometry : angle 0.53764 (17895) SS BOND : bond 0.00350 ( 8) SS BOND : angle 0.89164 ( 16) hydrogen bonds : bond 0.04554 ( 719) hydrogen bonds : angle 4.97617 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: C 175 MET cc_start: 0.8767 (tpp) cc_final: 0.8294 (tpt) REVERT: E 33 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8997 (tm) REVERT: E 47 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9024 (mp) REVERT: E 107 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8818 (ttmm) REVERT: E 123 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 155 ARG cc_start: 0.8440 (ptm160) cc_final: 0.8111 (ppp80) REVERT: E 188 ARG cc_start: 0.9111 (ptm160) cc_final: 0.8538 (ptp-170) REVERT: D 13 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8198 (mmpt) REVERT: D 73 ASP cc_start: 0.8917 (t0) cc_final: 0.8629 (t0) REVERT: D 77 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8271 (mtm110) REVERT: D 81 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8793 (ttp) REVERT: D 82 GLU cc_start: 0.8707 (tp30) cc_final: 0.8381 (tp30) REVERT: F 39 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8894 (tt0) REVERT: F 73 ASP cc_start: 0.8753 (t0) cc_final: 0.8269 (t0) REVERT: F 75 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.9038 (p) REVERT: A 331 ASP cc_start: 0.9094 (m-30) cc_final: 0.8851 (p0) outliers start: 40 outliers final: 19 residues processed: 153 average time/residue: 0.8109 time to fit residues: 138.1162 Evaluate side-chains 148 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** 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 = 0.3527 r_free = 0.3527 target = 0.091775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064361 restraints weight = 66090.239| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.37 r_work: 0.2849 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13175 Z= 0.178 Angle : 0.523 5.592 17911 Z= 0.276 Chirality : 0.039 0.156 2108 Planarity : 0.003 0.045 2203 Dihedral : 6.525 59.995 1866 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.23 % Allowed : 23.12 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.74 (0.22), residues: 1665 helix: 2.27 (0.19), residues: 742 sheet: -0.26 (0.31), residues: 310 loop : -1.38 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.012 0.001 TYR F 106 PHE 0.022 0.001 PHE A 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00403 (13167) covalent geometry : angle 0.52281 (17895) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.70494 ( 16) hydrogen bonds : bond 0.04407 ( 719) hydrogen bonds : angle 4.70894 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 MET cc_start: 0.8676 (tpp) cc_final: 0.8168 (tpt) REVERT: E 33 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8903 (tm) REVERT: E 107 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8611 (ttmm) REVERT: E 123 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8149 (tm-30) REVERT: E 175 MET cc_start: 0.7991 (tpt) cc_final: 0.7733 (tpt) REVERT: E 188 ARG cc_start: 0.9123 (ptm160) cc_final: 0.8534 (ptp-170) REVERT: D 13 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8066 (mmpt) REVERT: D 73 ASP cc_start: 0.8882 (t0) cc_final: 0.8577 (t0) REVERT: D 81 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8778 (ttp) REVERT: D 82 GLU cc_start: 0.8565 (tp30) cc_final: 0.8259 (tp30) REVERT: F 3 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (pp30) REVERT: F 39 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8780 (tt0) REVERT: F 73 ASP cc_start: 0.8694 (t0) cc_final: 0.8205 (t0) outliers start: 46 outliers final: 20 residues processed: 163 average time/residue: 0.7737 time to fit residues: 141.0684 Evaluate side-chains 150 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.091684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064342 restraints weight = 66052.987| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.37 r_work: 0.2838 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13175 Z= 0.159 Angle : 0.511 4.846 17911 Z= 0.268 Chirality : 0.039 0.154 2108 Planarity : 0.003 0.042 2203 Dihedral : 6.297 55.767 1866 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.37 % Allowed : 22.77 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.80 (0.22), residues: 1665 helix: 2.30 (0.19), residues: 742 sheet: -0.22 (0.31), residues: 310 loop : -1.33 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.011 0.001 TYR F 106 PHE 0.023 0.001 PHE A 327 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00359 (13167) covalent geometry : angle 0.51056 (17895) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.65435 ( 16) hydrogen bonds : bond 0.04157 ( 719) hydrogen bonds : angle 4.51405 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8641 (tm) REVERT: C 175 MET cc_start: 0.8697 (tpp) cc_final: 0.8116 (tpt) REVERT: E 33 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8900 (tm) REVERT: E 107 LYS cc_start: 0.9092 (ttmm) cc_final: 0.8759 (ttmm) REVERT: E 123 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 175 MET cc_start: 0.7911 (tpt) cc_final: 0.7566 (tpt) REVERT: E 188 ARG cc_start: 0.9124 (ptm160) cc_final: 0.8500 (ptp-170) REVERT: D 73 ASP cc_start: 0.8885 (t0) cc_final: 0.8598 (t0) REVERT: D 81 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8841 (ttp) REVERT: F 3 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8543 (pp30) REVERT: F 39 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8747 (tt0) REVERT: F 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8262 (t0) REVERT: B 331 ASP cc_start: 0.9145 (m-30) cc_final: 0.8810 (p0) REVERT: A 331 ASP cc_start: 0.9117 (m-30) cc_final: 0.8822 (p0) outliers start: 48 outliers final: 19 residues processed: 165 average time/residue: 0.7802 time to fit residues: 143.4500 Evaluate side-chains 152 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** 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 = 0.3541 r_free = 0.3541 target = 0.092514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065243 restraints weight = 65647.960| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.38 r_work: 0.2858 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13175 Z= 0.123 Angle : 0.492 4.498 17911 Z= 0.257 Chirality : 0.038 0.140 2108 Planarity : 0.003 0.039 2203 Dihedral : 6.055 52.746 1866 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.81 % Allowed : 23.26 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.93 (0.22), residues: 1665 helix: 2.42 (0.19), residues: 742 sheet: -0.12 (0.31), residues: 310 loop : -1.29 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.010 0.001 TYR F 106 PHE 0.021 0.001 PHE B 327 TRP 0.011 0.001 TRP A 98 HIS 0.001 0.000 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00274 (13167) covalent geometry : angle 0.49233 (17895) SS BOND : bond 0.00201 ( 8) SS BOND : angle 0.58652 ( 16) hydrogen bonds : bond 0.03842 ( 719) hydrogen bonds : angle 4.33435 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8640 (tm) REVERT: C 175 MET cc_start: 0.8728 (tpp) cc_final: 0.8048 (tpt) REVERT: E 33 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8856 (tm) REVERT: E 107 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8812 (ttmm) REVERT: E 123 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8166 (tm-30) REVERT: E 175 MET cc_start: 0.7838 (tpt) cc_final: 0.7508 (tpt) REVERT: E 188 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8456 (ptp-170) REVERT: D 13 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8208 (mmpt) REVERT: D 73 ASP cc_start: 0.8896 (t0) cc_final: 0.8611 (t0) REVERT: D 77 ARG cc_start: 0.8473 (mtm110) cc_final: 0.8085 (mtm110) REVERT: F 3 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8548 (pp30) REVERT: F 39 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8745 (tt0) REVERT: F 73 ASP cc_start: 0.8544 (t0) cc_final: 0.8299 (t0) REVERT: A 331 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8808 (p0) outliers start: 40 outliers final: 19 residues processed: 165 average time/residue: 0.7742 time to fit residues: 143.3530 Evaluate side-chains 149 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064102 restraints weight = 66247.804| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.38 r_work: 0.2832 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13175 Z= 0.180 Angle : 0.519 5.365 17911 Z= 0.273 Chirality : 0.039 0.189 2108 Planarity : 0.003 0.038 2203 Dihedral : 6.132 57.319 1866 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.81 % Allowed : 23.96 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.88 (0.22), residues: 1665 helix: 2.35 (0.19), residues: 746 sheet: -0.10 (0.31), residues: 310 loop : -1.35 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.011 0.001 TYR E 86 PHE 0.024 0.001 PHE A 327 TRP 0.010 0.001 TRP A 98 HIS 0.002 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00410 (13167) covalent geometry : angle 0.51881 (17895) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.69009 ( 16) hydrogen bonds : bond 0.04007 ( 719) hydrogen bonds : angle 4.34947 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8801 (tm) REVERT: C 175 MET cc_start: 0.8734 (tpp) cc_final: 0.8315 (tpt) REVERT: E 33 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (tm) REVERT: E 107 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8818 (ttmm) REVERT: E 123 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 149 LYS cc_start: 0.5807 (mptt) cc_final: 0.4787 (pptt) REVERT: E 175 MET cc_start: 0.7834 (tpt) cc_final: 0.7543 (tpt) REVERT: E 188 ARG cc_start: 0.9122 (ptm160) cc_final: 0.8475 (ptp-170) REVERT: D 73 ASP cc_start: 0.8876 (t0) cc_final: 0.8598 (t0) REVERT: D 77 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8117 (mtm110) REVERT: D 82 GLU cc_start: 0.8624 (tp30) cc_final: 0.8363 (mm-30) REVERT: F 3 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8545 (pp30) REVERT: F 39 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: F 73 ASP cc_start: 0.8547 (t0) cc_final: 0.8295 (t0) REVERT: B 331 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8817 (p0) REVERT: A 331 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8802 (p0) outliers start: 40 outliers final: 22 residues processed: 152 average time/residue: 0.7329 time to fit residues: 125.5078 Evaluate side-chains 154 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** 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 = 0.3524 r_free = 0.3524 target = 0.091412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064136 restraints weight = 66159.289| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.38 r_work: 0.2838 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13175 Z= 0.157 Angle : 0.513 5.663 17911 Z= 0.270 Chirality : 0.039 0.156 2108 Planarity : 0.003 0.038 2203 Dihedral : 6.026 54.523 1866 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.67 % Allowed : 23.75 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.89 (0.22), residues: 1665 helix: 2.37 (0.19), residues: 746 sheet: -0.13 (0.32), residues: 304 loop : -1.32 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.011 0.001 TYR F 106 PHE 0.024 0.001 PHE A 327 TRP 0.010 0.001 TRP A 98 HIS 0.001 0.000 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00357 (13167) covalent geometry : angle 0.51329 (17895) SS BOND : bond 0.00209 ( 8) SS BOND : angle 0.63617 ( 16) hydrogen bonds : bond 0.03911 ( 719) hydrogen bonds : angle 4.28781 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.612 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: C 33 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8715 (tm) REVERT: C 175 MET cc_start: 0.8752 (tpp) cc_final: 0.8325 (tpt) REVERT: E 24 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8172 (ttm110) REVERT: E 107 LYS cc_start: 0.9167 (ttmm) cc_final: 0.8840 (ttmm) REVERT: E 123 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8113 (tm-30) REVERT: E 149 LYS cc_start: 0.5788 (mptt) cc_final: 0.4818 (pptt) REVERT: E 188 ARG cc_start: 0.9112 (ptm160) cc_final: 0.8451 (ptp-170) REVERT: D 73 ASP cc_start: 0.8869 (t0) cc_final: 0.8586 (t0) REVERT: D 77 ARG cc_start: 0.8487 (mtm110) cc_final: 0.8123 (mtm110) REVERT: D 82 GLU cc_start: 0.8605 (tp30) cc_final: 0.8371 (mm-30) REVERT: F 3 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8559 (pp30) REVERT: F 39 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8747 (tt0) REVERT: F 73 ASP cc_start: 0.8571 (t0) cc_final: 0.8316 (t0) outliers start: 38 outliers final: 22 residues processed: 157 average time/residue: 0.7446 time to fit residues: 131.2394 Evaluate side-chains 149 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 158 optimal weight: 0.0070 chunk 119 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063971 restraints weight = 66718.596| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.37 r_work: 0.2829 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13175 Z= 0.170 Angle : 0.529 7.334 17911 Z= 0.277 Chirality : 0.039 0.152 2108 Planarity : 0.003 0.038 2203 Dihedral : 5.990 52.571 1866 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.32 % Allowed : 24.03 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.87 (0.22), residues: 1665 helix: 2.36 (0.19), residues: 746 sheet: -0.14 (0.32), residues: 306 loop : -1.35 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 77 TYR 0.011 0.001 TYR F 106 PHE 0.027 0.001 PHE B 327 TRP 0.010 0.001 TRP A 98 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00388 (13167) covalent geometry : angle 0.52932 (17895) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.68838 ( 16) hydrogen bonds : bond 0.03965 ( 719) hydrogen bonds : angle 4.28403 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8810 (tm) REVERT: C 175 MET cc_start: 0.8751 (tpp) cc_final: 0.8051 (tpt) REVERT: E 107 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8839 (ttmm) REVERT: E 188 ARG cc_start: 0.9132 (ptm160) cc_final: 0.8431 (ptp-110) REVERT: D 73 ASP cc_start: 0.8865 (t0) cc_final: 0.8582 (t0) REVERT: D 77 ARG cc_start: 0.8501 (mtm110) cc_final: 0.8136 (mtm110) REVERT: D 82 GLU cc_start: 0.8570 (tp30) cc_final: 0.8340 (mm-30) REVERT: F 3 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8583 (pp30) REVERT: F 39 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: F 73 ASP cc_start: 0.8585 (t0) cc_final: 0.8335 (t0) REVERT: B 331 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8811 (p0) REVERT: A 331 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8783 (p0) outliers start: 33 outliers final: 20 residues processed: 149 average time/residue: 0.7865 time to fit residues: 131.1329 Evaluate side-chains 149 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.091989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064833 restraints weight = 65791.845| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.37 r_work: 0.2848 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13175 Z= 0.128 Angle : 0.516 6.953 17911 Z= 0.269 Chirality : 0.038 0.139 2108 Planarity : 0.003 0.038 2203 Dihedral : 5.857 53.904 1866 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.90 % Allowed : 24.74 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.96 (0.22), residues: 1665 helix: 2.44 (0.19), residues: 746 sheet: -0.11 (0.32), residues: 306 loop : -1.30 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 24 TYR 0.010 0.001 TYR F 106 PHE 0.022 0.001 PHE A 327 TRP 0.011 0.001 TRP B 98 HIS 0.001 0.000 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00290 (13167) covalent geometry : angle 0.51620 (17895) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.62009 ( 16) hydrogen bonds : bond 0.03741 ( 719) hydrogen bonds : angle 4.19523 ( 2067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.685 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: C 33 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8672 (tm) REVERT: C 175 MET cc_start: 0.8747 (tpp) cc_final: 0.8068 (tpt) REVERT: E 107 LYS cc_start: 0.9173 (ttmm) cc_final: 0.8806 (ttmm) REVERT: E 149 LYS cc_start: 0.6062 (mptt) cc_final: 0.4970 (pptt) REVERT: E 188 ARG cc_start: 0.9134 (ptm160) cc_final: 0.8438 (ptp-110) REVERT: D 73 ASP cc_start: 0.8861 (t0) cc_final: 0.8585 (t0) REVERT: D 77 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8163 (mtm110) REVERT: D 82 GLU cc_start: 0.8550 (tp30) cc_final: 0.8319 (mm-30) REVERT: D 199 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: F 3 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8591 (pp30) REVERT: F 39 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: F 43 GLN cc_start: 0.7460 (mt0) cc_final: 0.6985 (mp10) REVERT: F 73 ASP cc_start: 0.8582 (t0) cc_final: 0.8329 (t0) REVERT: A 331 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8789 (p0) outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 0.7735 time to fit residues: 129.8701 Evaluate side-chains 144 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.091751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064634 restraints weight = 66280.595| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.36 r_work: 0.2839 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13175 Z= 0.158 Angle : 0.533 8.218 17911 Z= 0.278 Chirality : 0.038 0.144 2108 Planarity : 0.003 0.038 2203 Dihedral : 5.882 54.913 1866 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.76 % Allowed : 25.09 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.93 (0.22), residues: 1665 helix: 2.42 (0.19), residues: 746 sheet: -0.12 (0.32), residues: 306 loop : -1.32 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 24 TYR 0.014 0.001 TYR E 186 PHE 0.024 0.001 PHE A 327 TRP 0.010 0.001 TRP B 98 HIS 0.001 0.000 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00360 (13167) covalent geometry : angle 0.53312 (17895) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.66662 ( 16) hydrogen bonds : bond 0.03821 ( 719) hydrogen bonds : angle 4.20547 ( 2067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8814 (tm) REVERT: C 175 MET cc_start: 0.8768 (tpp) cc_final: 0.8076 (tpt) REVERT: E 149 LYS cc_start: 0.6097 (mptt) cc_final: 0.4955 (pptt) REVERT: E 188 ARG cc_start: 0.9134 (ptm160) cc_final: 0.8427 (ptp-110) REVERT: D 73 ASP cc_start: 0.8855 (t0) cc_final: 0.8572 (t0) REVERT: D 77 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8155 (mtm110) REVERT: F 3 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8593 (pp30) REVERT: F 39 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: F 43 GLN cc_start: 0.7460 (mt0) cc_final: 0.6998 (mp10) REVERT: F 73 ASP cc_start: 0.8587 (t0) cc_final: 0.8332 (t0) REVERT: B 331 ASP cc_start: 0.9148 (m-30) cc_final: 0.8811 (p0) REVERT: A 331 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8795 (p0) outliers start: 25 outliers final: 19 residues processed: 142 average time/residue: 0.8060 time to fit residues: 127.8830 Evaluate side-chains 147 residues out of total 1423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 67 optimal weight: 0.0170 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064874 restraints weight = 66044.198| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.35 r_work: 0.2848 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13175 Z= 0.136 Angle : 0.527 9.425 17911 Z= 0.274 Chirality : 0.038 0.139 2108 Planarity : 0.003 0.038 2203 Dihedral : 5.787 56.114 1864 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 1.83 % Allowed : 25.02 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.97 (0.22), residues: 1665 helix: 2.45 (0.19), residues: 746 sheet: -0.10 (0.32), residues: 306 loop : -1.30 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 24 TYR 0.010 0.001 TYR F 106 PHE 0.022 0.001 PHE A 327 TRP 0.010 0.001 TRP B 98 HIS 0.001 0.000 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00310 (13167) covalent geometry : angle 0.52717 (17895) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.73932 ( 16) hydrogen bonds : bond 0.03723 ( 719) hydrogen bonds : angle 4.15899 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5368.22 seconds wall clock time: 92 minutes 11.61 seconds (5531.61 seconds total)