Starting phenix.real_space_refine on Tue Feb 3 21:57:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.map" model { file = "/net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyi_64611/02_2026/9uyi_64611.cif" } resolution = 3.2 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= 0.035 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 19 5.16 5 C 4590 2.51 5 N 1217 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7150 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2469 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 25, 'TRANS': 306} Chain breaks: 4 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 15, 'ARG:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 812 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 109} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2095 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 467 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'TRP:plan': 5, 'PHE:plan': 8, 'ASN:plan1': 5, 'HIS:plan': 3, 'ARG:plan': 4, 'TYR:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 177 Chain: "C" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7150 At special positions: 0 Unit cell: (78.183, 110.313, 145.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 6 15.00 O 1318 8.00 N 1217 7.00 C 4590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " 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: 0.71 Conformation dependent library (CDL) restraints added in 275.2 milliseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 23.4% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'B' and resid 86 through 90 removed outlier: 4.023A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 61 Proline residue: R 54 - end of helix removed outlier: 3.616A pdb=" N VAL R 59 " --> pdb=" O GLY R 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 99 removed outlier: 3.902A pdb=" N PHE R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 109 through 141 removed outlier: 4.179A pdb=" N PHE R 115 " --> pdb=" O LYS R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 174 Proline residue: R 171 - end of helix removed outlier: 3.560A pdb=" N TYR R 174 " --> pdb=" O GLY R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 213 Processing helix chain 'R' and resid 215 through 230 removed outlier: 3.945A pdb=" N CYS R 228 " --> pdb=" O ILE R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 275 removed outlier: 3.839A pdb=" N TRP R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Proline residue: R 261 - end of helix Processing helix chain 'R' and resid 285 through 305 removed outlier: 4.072A pdb=" N SER R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 307 through 316 removed outlier: 3.526A pdb=" N GLN R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.087A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.704A pdb=" N VAL A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 10 " --> pdb=" O ALA R1361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.104A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.418A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.418A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.697A pdb=" N HIS A 219 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 202 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.767A pdb=" N VAL A 343 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 325 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY A 316 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 241 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE A 318 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 239 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 320 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN A 237 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 322 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A 235 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS A 324 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 233 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS A 326 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE A 231 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 328 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 227 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 249 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.565A pdb=" N LEU B 80 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.578A pdb=" N ASN B 96 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.609A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.647A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.750A pdb=" N GLN C 91 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.662A pdb=" N GLN C 127 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 149 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.048A pdb=" N TRP C 171 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG C 162 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 233 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ARG C 224 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU C 231 " --> pdb=" O ARG C 224 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 792 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: 0.98 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2259 1.35 - 1.46: 1839 1.46 - 1.58: 3180 1.58 - 1.70: 23 1.70 - 1.81: 25 Bond restraints: 7326 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O2P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3P TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 7321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 9907 2.49 - 4.98: 107 4.98 - 7.47: 13 7.47 - 9.97: 2 9.97 - 12.46: 2 Bond angle restraints: 10031 Sorted by residual: angle pdb=" N ALA L 155 " pdb=" CA ALA L 155 " pdb=" C ALA L 155 " ideal model delta sigma weight residual 114.75 109.20 5.55 1.26e+00 6.30e-01 1.94e+01 angle pdb=" CB TPO R1360 " pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 119.31 106.85 12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" CB TPO R1359 " pdb=" OG1 TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 119.31 107.40 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA ALA L 155 " pdb=" C ALA L 155 " pdb=" N PHE L 156 " ideal model delta sigma weight residual 119.80 115.47 4.33 1.34e+00 5.57e-01 1.05e+01 angle pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " pdb=" O1P TPO R1360 " ideal model delta sigma weight residual 100.43 109.53 -9.10 3.00e+00 1.11e-01 9.21e+00 ... (remaining 10026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 3917 17.67 - 35.34: 289 35.34 - 53.01: 50 53.01 - 70.68: 7 70.68 - 88.35: 7 Dihedral angle restraints: 4270 sinusoidal: 1436 harmonic: 2834 Sorted by residual: dihedral pdb=" CA LYS R 66 " pdb=" C LYS R 66 " pdb=" N TRP R 67 " pdb=" CA TRP R 67 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE L 150 " pdb=" C PHE L 150 " pdb=" N PRO L 151 " pdb=" CA PRO L 151 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA HIS R 141 " pdb=" C HIS R 141 " pdb=" N PRO R 142 " pdb=" CA PRO R 142 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 716 0.029 - 0.057: 269 0.057 - 0.085: 114 0.085 - 0.114: 66 0.114 - 0.142: 14 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CB VAL R 233 " pdb=" CA VAL R 233 " pdb=" CG1 VAL R 233 " pdb=" CG2 VAL R 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB VAL B 63 " pdb=" CA VAL B 63 " pdb=" CG1 VAL B 63 " pdb=" CG2 VAL B 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CB ILE A 241 " pdb=" CA ILE A 241 " pdb=" CG1 ILE A 241 " pdb=" CG2 ILE A 241 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1176 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 170 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO R 171 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 263 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 264 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 138 " -0.014 2.00e-02 2.50e+03 1.66e-02 4.15e+00 pdb=" CG HIS R 138 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS R 138 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS R 138 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS R 138 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS R 138 " -0.002 2.00e-02 2.50e+03 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 114 2.68 - 3.23: 6781 3.23 - 3.79: 10526 3.79 - 4.34: 13762 4.34 - 4.90: 23214 Nonbonded interactions: 54397 Sorted by model distance: nonbonded pdb=" O TRP R 103 " pdb=" OG1 THR R 185 " model vdw 2.119 3.040 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.207 3.040 nonbonded pdb=" O TYR C 50 " pdb=" OH TYR C 92 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR B 52 " pdb=" OG1 THR B 56 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASN B 96 " pdb=" N THR B 97 " model vdw 2.223 3.120 ... (remaining 54392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7330 Z= 0.195 Angle : 0.670 12.457 10039 Z= 0.370 Chirality : 0.042 0.142 1179 Planarity : 0.005 0.062 1260 Dihedral : 12.964 88.349 2428 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.29), residues: 939 helix: 1.66 (0.38), residues: 191 sheet: -0.28 (0.35), residues: 269 loop : -1.57 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.023 0.001 TYR R 45 PHE 0.009 0.001 PHE L 156 TRP 0.018 0.001 TRP R 75 HIS 0.020 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7326) covalent geometry : angle 0.66983 (10031) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.44771 ( 8) hydrogen bonds : bond 0.21780 ( 286) hydrogen bonds : angle 7.71273 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.195 Fit side-chains REVERT: A 21 TYR cc_start: 0.8159 (m-80) cc_final: 0.7849 (m-80) REVERT: A 219 HIS cc_start: 0.6637 (t70) cc_final: 0.6289 (t70) REVERT: B 36 TRP cc_start: 0.7430 (m100) cc_final: 0.7063 (m100) REVERT: B 38 ARG cc_start: 0.8084 (ptt90) cc_final: 0.7519 (ptt180) REVERT: B 96 ASN cc_start: 0.8055 (t0) cc_final: 0.7851 (t0) REVERT: R 139 LEU cc_start: 0.7752 (tp) cc_final: 0.7424 (tp) REVERT: R 150 THR cc_start: 0.7376 (p) cc_final: 0.7166 (p) REVERT: R 190 ASN cc_start: 0.5534 (p0) cc_final: 0.4218 (p0) REVERT: R 277 TYR cc_start: 0.5291 (t80) cc_final: 0.4964 (t80) REVERT: C 84 PHE cc_start: 0.7986 (m-80) cc_final: 0.7606 (m-80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0775 time to fit residues: 17.3434 Evaluate side-chains 119 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS R 194 HIS R 274 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125736 restraints weight = 10317.351| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.38 r_work: 0.3476 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7330 Z= 0.205 Angle : 0.638 6.709 10039 Z= 0.335 Chirality : 0.046 0.161 1179 Planarity : 0.005 0.052 1260 Dihedral : 5.761 88.002 1052 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 1.73 % Allowed : 9.78 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.29), residues: 939 helix: 1.34 (0.38), residues: 200 sheet: -0.40 (0.35), residues: 258 loop : -1.64 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 285 TYR 0.018 0.002 TYR A 47 PHE 0.022 0.002 PHE A 87 TRP 0.012 0.001 TRP C 171 HIS 0.010 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 7326) covalent geometry : angle 0.63719 (10031) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.34643 ( 8) hydrogen bonds : bond 0.03761 ( 286) hydrogen bonds : angle 5.61284 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.206 Fit side-chains REVERT: A 219 HIS cc_start: 0.7046 (t70) cc_final: 0.6479 (t70) REVERT: A 222 ASN cc_start: 0.7523 (t0) cc_final: 0.7266 (t0) REVERT: B 36 TRP cc_start: 0.8281 (m100) cc_final: 0.7897 (m100) REVERT: R 103 TRP cc_start: 0.6566 (t-100) cc_final: 0.6103 (t-100) REVERT: R 118 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7883 (mm110) REVERT: R 243 ARG cc_start: 0.5543 (mmm160) cc_final: 0.4998 (mmm160) REVERT: C 12 LEU cc_start: 0.7964 (tt) cc_final: 0.7661 (tp) REVERT: C 83 ASP cc_start: 0.7581 (t70) cc_final: 0.7286 (t0) REVERT: C 201 ASN cc_start: 0.8107 (t0) cc_final: 0.7590 (t0) outliers start: 12 outliers final: 8 residues processed: 150 average time/residue: 0.0795 time to fit residues: 16.1421 Evaluate side-chains 121 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain C residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN R 204 HIS C 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.171933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124371 restraints weight = 10198.093| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.37 r_work: 0.3460 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7330 Z= 0.168 Angle : 0.597 6.672 10039 Z= 0.312 Chirality : 0.044 0.148 1179 Planarity : 0.004 0.052 1260 Dihedral : 5.754 85.093 1052 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.30 % Allowed : 14.24 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 939 helix: 1.55 (0.38), residues: 197 sheet: -0.53 (0.34), residues: 274 loop : -1.71 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 285 TYR 0.016 0.001 TYR A 47 PHE 0.019 0.002 PHE A 87 TRP 0.011 0.001 TRP C 171 HIS 0.022 0.002 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7326) covalent geometry : angle 0.59627 (10031) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.96343 ( 8) hydrogen bonds : bond 0.03652 ( 286) hydrogen bonds : angle 5.30754 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.189 Fit side-chains REVERT: A 65 ARG cc_start: 0.5529 (mpt180) cc_final: 0.5284 (mpt180) REVERT: A 219 HIS cc_start: 0.7110 (t70) cc_final: 0.6809 (t70) REVERT: A 222 ASN cc_start: 0.7525 (t0) cc_final: 0.7183 (t0) REVERT: B 82 MET cc_start: 0.7206 (mmt) cc_final: 0.6404 (mmt) REVERT: B 89 ASP cc_start: 0.8507 (t70) cc_final: 0.8221 (t70) REVERT: R 103 TRP cc_start: 0.6588 (t-100) cc_final: 0.6342 (t-100) REVERT: R 118 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7951 (mm110) REVERT: R 149 ARG cc_start: 0.7562 (mmm160) cc_final: 0.6763 (mmm160) REVERT: R 194 HIS cc_start: 0.6566 (m-70) cc_final: 0.6120 (t-90) REVERT: C 83 ASP cc_start: 0.7562 (t70) cc_final: 0.7295 (t0) REVERT: C 84 PHE cc_start: 0.8293 (m-80) cc_final: 0.7820 (m-80) REVERT: C 201 ASN cc_start: 0.8155 (t0) cc_final: 0.7512 (t0) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 0.0789 time to fit residues: 14.6889 Evaluate side-chains 128 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 78 ASN ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 ASN ** 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 = 0.4167 r_free = 0.4167 target = 0.173418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126084 restraints weight = 10292.902| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.40 r_work: 0.3487 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7330 Z= 0.121 Angle : 0.559 6.847 10039 Z= 0.290 Chirality : 0.042 0.143 1179 Planarity : 0.004 0.050 1260 Dihedral : 5.704 85.447 1052 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.59 % Allowed : 15.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 939 helix: 1.59 (0.37), residues: 197 sheet: -0.36 (0.34), residues: 268 loop : -1.74 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.021 0.001 TYR R 45 PHE 0.022 0.002 PHE L 154 TRP 0.008 0.001 TRP C 171 HIS 0.006 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7326) covalent geometry : angle 0.55807 (10031) SS BOND : bond 0.00237 ( 4) SS BOND : angle 1.39225 ( 8) hydrogen bonds : bond 0.03203 ( 286) hydrogen bonds : angle 5.07636 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.245 Fit side-chains REVERT: A 65 ARG cc_start: 0.5568 (mpt180) cc_final: 0.5299 (mpt180) REVERT: A 219 HIS cc_start: 0.7041 (t70) cc_final: 0.6538 (t70) REVERT: A 222 ASN cc_start: 0.7638 (t0) cc_final: 0.7312 (t0) REVERT: A 256 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7739 (tm-30) REVERT: R 118 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7968 (mm110) REVERT: R 149 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7011 (mmm160) REVERT: R 194 HIS cc_start: 0.6706 (m-70) cc_final: 0.6083 (t-90) REVERT: R 243 ARG cc_start: 0.5356 (mmm160) cc_final: 0.5017 (mmm160) REVERT: C 83 ASP cc_start: 0.7565 (t70) cc_final: 0.7250 (t0) REVERT: C 201 ASN cc_start: 0.8182 (t0) cc_final: 0.7409 (t0) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.0817 time to fit residues: 14.7317 Evaluate side-chains 122 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125623 restraints weight = 10205.222| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.38 r_work: 0.3473 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7330 Z= 0.127 Angle : 0.561 7.410 10039 Z= 0.291 Chirality : 0.043 0.161 1179 Planarity : 0.004 0.050 1260 Dihedral : 5.667 82.379 1052 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.31 % Allowed : 16.26 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 939 helix: 1.58 (0.37), residues: 199 sheet: -0.45 (0.34), residues: 274 loop : -1.69 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.017 0.001 TYR R 215 PHE 0.022 0.001 PHE A 87 TRP 0.009 0.001 TRP C 171 HIS 0.005 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7326) covalent geometry : angle 0.56037 (10031) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.33397 ( 8) hydrogen bonds : bond 0.03180 ( 286) hydrogen bonds : angle 4.98193 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.291 Fit side-chains REVERT: A 65 ARG cc_start: 0.5507 (mpt180) cc_final: 0.5233 (mpt180) REVERT: A 219 HIS cc_start: 0.7055 (t70) cc_final: 0.6738 (t70) REVERT: A 222 ASN cc_start: 0.7664 (t0) cc_final: 0.7328 (t0) REVERT: B 82 MET cc_start: 0.7253 (mmt) cc_final: 0.6467 (mmt) REVERT: R 118 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7887 (mm110) REVERT: R 149 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7064 (mmm160) REVERT: R 194 HIS cc_start: 0.6753 (m-70) cc_final: 0.6063 (t-90) REVERT: R 243 ARG cc_start: 0.5190 (mmm160) cc_final: 0.4814 (mmm160) REVERT: R 300 ASN cc_start: 0.7930 (m-40) cc_final: 0.7713 (m110) REVERT: C 83 ASP cc_start: 0.7597 (t70) cc_final: 0.7287 (t0) REVERT: C 201 ASN cc_start: 0.8207 (t0) cc_final: 0.7689 (t0) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.0958 time to fit residues: 16.5753 Evaluate side-chains 126 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125476 restraints weight = 10269.433| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.39 r_work: 0.3474 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7330 Z= 0.122 Angle : 0.560 7.777 10039 Z= 0.287 Chirality : 0.042 0.144 1179 Planarity : 0.004 0.049 1260 Dihedral : 5.628 81.055 1052 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.60 % Allowed : 17.41 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.29), residues: 939 helix: 1.69 (0.37), residues: 197 sheet: -0.34 (0.34), residues: 267 loop : -1.73 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.014 0.001 TYR A 47 PHE 0.035 0.002 PHE L 154 TRP 0.009 0.001 TRP C 171 HIS 0.004 0.001 HIS R 135 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7326) covalent geometry : angle 0.55934 (10031) SS BOND : bond 0.00231 ( 4) SS BOND : angle 1.10336 ( 8) hydrogen bonds : bond 0.03060 ( 286) hydrogen bonds : angle 4.87314 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.287 Fit side-chains REVERT: A 219 HIS cc_start: 0.7041 (t70) cc_final: 0.6521 (t70) REVERT: A 222 ASN cc_start: 0.7662 (t0) cc_final: 0.7319 (t0) REVERT: R 118 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7579 (mm-40) REVERT: R 149 ARG cc_start: 0.7535 (mmm160) cc_final: 0.7007 (mmm160) REVERT: R 194 HIS cc_start: 0.6699 (m-70) cc_final: 0.6070 (t-90) REVERT: R 243 ARG cc_start: 0.5216 (mmm160) cc_final: 0.4808 (mmm160) REVERT: C 83 ASP cc_start: 0.7587 (t70) cc_final: 0.7279 (t0) REVERT: C 201 ASN cc_start: 0.8262 (t0) cc_final: 0.7723 (t0) REVERT: C 204 TYR cc_start: 0.7155 (m-80) cc_final: 0.6700 (m-80) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.0853 time to fit residues: 15.4723 Evaluate side-chains 127 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** R 138 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 = 0.4168 r_free = 0.4168 target = 0.173260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125971 restraints weight = 10225.520| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.37 r_work: 0.3476 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7330 Z= 0.119 Angle : 0.557 8.139 10039 Z= 0.286 Chirality : 0.042 0.203 1179 Planarity : 0.004 0.049 1260 Dihedral : 5.548 80.378 1052 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.88 % Allowed : 17.70 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.29), residues: 939 helix: 1.59 (0.36), residues: 202 sheet: -0.33 (0.34), residues: 270 loop : -1.73 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.015 0.001 TYR A 47 PHE 0.024 0.001 PHE C 151 TRP 0.008 0.001 TRP C 171 HIS 0.004 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7326) covalent geometry : angle 0.55604 (10031) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.03250 ( 8) hydrogen bonds : bond 0.03004 ( 286) hydrogen bonds : angle 4.80615 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.301 Fit side-chains REVERT: L 154 PHE cc_start: 0.6097 (p90) cc_final: 0.5817 (p90) REVERT: A 219 HIS cc_start: 0.7050 (t70) cc_final: 0.6626 (t70) REVERT: A 222 ASN cc_start: 0.7664 (t0) cc_final: 0.7318 (t0) REVERT: R 45 TYR cc_start: 0.7558 (m-80) cc_final: 0.7327 (m-80) REVERT: R 118 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: R 149 ARG cc_start: 0.7634 (mmm160) cc_final: 0.7113 (mmm160) REVERT: R 243 ARG cc_start: 0.5205 (mmm160) cc_final: 0.4778 (mmm160) REVERT: C 83 ASP cc_start: 0.7515 (t70) cc_final: 0.7215 (t0) REVERT: C 201 ASN cc_start: 0.8273 (t0) cc_final: 0.7715 (t0) outliers start: 20 outliers final: 18 residues processed: 129 average time/residue: 0.0865 time to fit residues: 15.1653 Evaluate side-chains 125 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121433 restraints weight = 10375.391| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.39 r_work: 0.3416 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7330 Z= 0.190 Angle : 0.619 9.551 10039 Z= 0.317 Chirality : 0.044 0.198 1179 Planarity : 0.004 0.048 1260 Dihedral : 5.724 74.009 1052 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.60 % Allowed : 18.56 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.29), residues: 939 helix: 1.61 (0.38), residues: 192 sheet: -0.45 (0.33), residues: 280 loop : -1.79 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 71 TYR 0.022 0.001 TYR A 47 PHE 0.025 0.002 PHE C 151 TRP 0.011 0.001 TRP C 171 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7326) covalent geometry : angle 0.61870 (10031) SS BOND : bond 0.00275 ( 4) SS BOND : angle 1.27187 ( 8) hydrogen bonds : bond 0.03366 ( 286) hydrogen bonds : angle 4.94376 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.290 Fit side-chains REVERT: A 85 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6591 (mm-40) REVERT: A 219 HIS cc_start: 0.7061 (t70) cc_final: 0.6530 (t70) REVERT: A 222 ASN cc_start: 0.7770 (t0) cc_final: 0.7407 (t0) REVERT: R 118 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7860 (mm110) REVERT: R 149 ARG cc_start: 0.7618 (mmm160) cc_final: 0.7064 (mmm160) REVERT: R 243 ARG cc_start: 0.5268 (mmm160) cc_final: 0.4813 (mmm160) REVERT: C 83 ASP cc_start: 0.7678 (t70) cc_final: 0.7330 (t0) REVERT: C 167 LYS cc_start: 0.7628 (mmmt) cc_final: 0.6850 (mtpt) REVERT: C 201 ASN cc_start: 0.8256 (t0) cc_final: 0.7694 (t0) outliers start: 25 outliers final: 20 residues processed: 132 average time/residue: 0.0884 time to fit residues: 15.8299 Evaluate side-chains 130 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.0070 chunk 82 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125018 restraints weight = 10222.604| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.37 r_work: 0.3465 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7330 Z= 0.121 Angle : 0.578 8.609 10039 Z= 0.295 Chirality : 0.043 0.193 1179 Planarity : 0.004 0.048 1260 Dihedral : 5.596 76.289 1052 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.88 % Allowed : 19.57 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.29), residues: 939 helix: 1.65 (0.37), residues: 201 sheet: -0.49 (0.33), residues: 280 loop : -1.77 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 202 TYR 0.017 0.001 TYR A 47 PHE 0.041 0.002 PHE L 154 TRP 0.010 0.001 TRP C 171 HIS 0.004 0.001 HIS R 135 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7326) covalent geometry : angle 0.57793 (10031) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.99926 ( 8) hydrogen bonds : bond 0.03006 ( 286) hydrogen bonds : angle 4.82787 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.263 Fit side-chains REVERT: A 85 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6683 (mm110) REVERT: A 87 PHE cc_start: 0.7376 (t80) cc_final: 0.7158 (t80) REVERT: A 219 HIS cc_start: 0.7068 (t70) cc_final: 0.6534 (t70) REVERT: A 222 ASN cc_start: 0.7696 (t0) cc_final: 0.7353 (t0) REVERT: R 45 TYR cc_start: 0.7604 (m-80) cc_final: 0.7382 (m-80) REVERT: R 118 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7554 (mm-40) REVERT: R 149 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7411 (mmm160) REVERT: R 243 ARG cc_start: 0.5219 (mmm160) cc_final: 0.4763 (mmm160) REVERT: C 83 ASP cc_start: 0.7583 (t70) cc_final: 0.7330 (t0) REVERT: C 167 LYS cc_start: 0.7597 (mmmt) cc_final: 0.6782 (mtpt) REVERT: C 201 ASN cc_start: 0.8297 (t0) cc_final: 0.7726 (t0) REVERT: C 204 TYR cc_start: 0.7167 (m-80) cc_final: 0.6621 (m-80) outliers start: 20 outliers final: 18 residues processed: 128 average time/residue: 0.0852 time to fit residues: 14.9260 Evaluate side-chains 127 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 10.0000 chunk 92 optimal weight: 0.0570 chunk 60 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124978 restraints weight = 10288.218| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.40 r_work: 0.3466 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7330 Z= 0.122 Angle : 0.570 8.572 10039 Z= 0.293 Chirality : 0.043 0.186 1179 Planarity : 0.004 0.048 1260 Dihedral : 5.538 77.818 1052 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.88 % Allowed : 20.00 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.29), residues: 939 helix: 1.56 (0.37), residues: 202 sheet: -0.49 (0.33), residues: 280 loop : -1.76 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.016 0.001 TYR A 47 PHE 0.027 0.001 PHE C 151 TRP 0.009 0.001 TRP C 171 HIS 0.004 0.001 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7326) covalent geometry : angle 0.56978 (10031) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.92793 ( 8) hydrogen bonds : bond 0.03004 ( 286) hydrogen bonds : angle 4.74784 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.297 Fit side-chains REVERT: L 154 PHE cc_start: 0.6182 (p90) cc_final: 0.5963 (p90) REVERT: A 85 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6526 (mm110) REVERT: A 87 PHE cc_start: 0.7311 (t80) cc_final: 0.7099 (t80) REVERT: A 219 HIS cc_start: 0.7043 (t70) cc_final: 0.6512 (t70) REVERT: A 222 ASN cc_start: 0.7697 (t0) cc_final: 0.7348 (t0) REVERT: B 36 TRP cc_start: 0.8343 (m100) cc_final: 0.7987 (m100) REVERT: R 45 TYR cc_start: 0.7611 (m-80) cc_final: 0.7386 (m-80) REVERT: R 118 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7562 (mm-40) REVERT: R 149 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7391 (mmm160) REVERT: R 243 ARG cc_start: 0.5258 (mmm160) cc_final: 0.4801 (mmm160) REVERT: C 83 ASP cc_start: 0.7611 (t70) cc_final: 0.7365 (t0) REVERT: C 101 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7465 (mt0) REVERT: C 167 LYS cc_start: 0.7571 (mmmt) cc_final: 0.6760 (mtpt) REVERT: C 201 ASN cc_start: 0.8322 (t0) cc_final: 0.7753 (t0) REVERT: C 204 TYR cc_start: 0.7039 (m-80) cc_final: 0.6517 (m-80) outliers start: 20 outliers final: 17 residues processed: 131 average time/residue: 0.0835 time to fit residues: 15.0914 Evaluate side-chains 131 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain R residue 118 GLN Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 177 ASP Chi-restraints excluded: chain R residue 274 HIS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125215 restraints weight = 10199.785| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.36 r_work: 0.3473 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7330 Z= 0.122 Angle : 0.571 8.846 10039 Z= 0.292 Chirality : 0.042 0.180 1179 Planarity : 0.004 0.048 1260 Dihedral : 5.510 78.243 1052 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.73 % Allowed : 19.86 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.29), residues: 939 helix: 1.60 (0.37), residues: 201 sheet: -0.47 (0.33), residues: 279 loop : -1.75 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.014 0.001 TYR A 47 PHE 0.027 0.001 PHE C 151 TRP 0.010 0.001 TRP C 171 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7326) covalent geometry : angle 0.57070 (10031) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.93976 ( 8) hydrogen bonds : bond 0.03006 ( 286) hydrogen bonds : angle 4.73499 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.18 seconds wall clock time: 33 minutes 8.61 seconds (1988.61 seconds total)