Starting phenix.real_space_refine on Thu Feb 5 11:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.map" model { file = "/net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4g_62058/02_2026/9k4g_62058.cif" } resolution = 2.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 10521 2.51 5 N 2940 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 16807 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "C" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "G" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "H" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "I" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2401 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 307} Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 16807 At special positions: 0 Unit cell: (205.92, 165, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 3311 8.00 N 2940 7.00 C 10521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.30 Conformation dependent library (CDL) restraints added in 790.1 milliseconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 28 sheets defined 29.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 96 through 103 removed outlier: 4.280A pdb=" N LEU A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 142 removed outlier: 3.625A pdb=" N ALA A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.743A pdb=" N PHE A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.062A pdb=" N ASN B 29 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 removed outlier: 4.232A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 141 removed outlier: 4.211A pdb=" N GLY B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.527A pdb=" N PHE B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.685A pdb=" N LEU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.722A pdb=" N LEU C 100 " --> pdb=" O PRO C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 141 removed outlier: 3.566A pdb=" N GLY C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 168 removed outlier: 3.595A pdb=" N PHE C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 removed outlier: 4.482A pdb=" N THR C 172 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 removed outlier: 4.014A pdb=" N LEU C 184 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 96 through 103 removed outlier: 4.090A pdb=" N LEU D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 141 removed outlier: 4.040A pdb=" N ALA D 112 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 180 through 193 removed outlier: 3.833A pdb=" N LEU D 184 " --> pdb=" O HIS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.020A pdb=" N VAL D 204 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'G' and resid 28 through 33 Processing helix chain 'G' and resid 96 through 103 removed outlier: 4.212A pdb=" N LEU G 100 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 142 removed outlier: 3.903A pdb=" N ALA G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 168 removed outlier: 3.854A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN G 161 " --> pdb=" O GLN G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 174 removed outlier: 4.440A pdb=" N THR G 172 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 193 removed outlier: 3.555A pdb=" N LEU G 184 " --> pdb=" O HIS G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 227 through 231 Processing helix chain 'G' and resid 293 through 299 Processing helix chain 'H' and resid 28 through 33 Processing helix chain 'H' and resid 96 through 103 removed outlier: 4.214A pdb=" N LEU H 100 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 141 removed outlier: 3.929A pdb=" N ALA H 112 " --> pdb=" O GLN H 108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 165 Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.761A pdb=" N LEU H 184 " --> pdb=" O HIS H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 222 No H-bonds generated for 'chain 'H' and resid 220 through 222' Processing helix chain 'H' and resid 293 through 299 Processing helix chain 'H' and resid 309 through 313 Processing helix chain 'I' and resid 28 through 33 Processing helix chain 'I' and resid 96 through 103 removed outlier: 4.322A pdb=" N LEU I 100 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 142 removed outlier: 4.205A pdb=" N GLY I 111 " --> pdb=" O PRO I 107 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY I 120 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 removed outlier: 3.700A pdb=" N ASN I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 174 removed outlier: 4.550A pdb=" N THR I 172 " --> pdb=" O ASP I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.972A pdb=" N LEU I 184 " --> pdb=" O HIS I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.935A pdb=" N VAL I 204 " --> pdb=" O PHE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'I' and resid 227 through 231 Processing helix chain 'I' and resid 284 through 289 Processing helix chain 'I' and resid 293 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 40 current: chain 'A' and resid 265 through 277 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 146 removed outlier: 6.542A pdb=" N HIS A 145 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 14 removed outlier: 6.537A pdb=" N ASP B 11 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA C 51 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 13 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N TRP C 53 " --> pdb=" O ALA B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 94 current: chain 'C' and resid 265 through 278 Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 39 current: chain 'B' and resid 80 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 80 through 89 current: chain 'B' and resid 265 through 278 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 62 current: chain 'G' and resid 267 through 278 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 146 removed outlier: 7.073A pdb=" N HIS B 145 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.547A pdb=" N ALA B 210 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 14 through 18 current: chain 'D' and resid 78 through 90 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 78 through 90 current: chain 'D' and resid 267 through 278 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 144 through 147 current: chain 'C' and resid 215 through 217 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 215 through 217 current: chain 'C' and resid 232 through 238 Processing sheet with id=AB4, first strand: chain 'C' and resid 281 through 283 Processing sheet with id=AB5, first strand: chain 'D' and resid 14 through 18 removed outlier: 3.558A pdb=" N TRP H 53 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET D 17 " --> pdb=" O TRP H 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB7, first strand: chain 'D' and resid 144 through 146 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 144 through 146 current: chain 'D' and resid 215 through 217 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 217 current: chain 'D' and resid 232 through 238 Processing sheet with id=AB8, first strand: chain 'D' and resid 281 through 283 Processing sheet with id=AB9, first strand: chain 'G' and resid 50 through 53 Processing sheet with id=AC1, first strand: chain 'G' and resid 61 through 62 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 61 through 62 current: chain 'I' and resid 78 through 90 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 78 through 90 current: chain 'I' and resid 265 through 278 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 74 through 75 removed outlier: 7.139A pdb=" N LYS G 74 " --> pdb=" O ASN I 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 144 through 147 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 144 through 147 current: chain 'G' and resid 232 through 238 Processing sheet with id=AC4, first strand: chain 'G' and resid 281 through 283 Processing sheet with id=AC5, first strand: chain 'H' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 36 through 39 current: chain 'H' and resid 265 through 278 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 144 through 146 removed outlier: 6.018A pdb=" N HIS H 145 " --> pdb=" O VAL H 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 177 through 179 Processing sheet with id=AC8, first strand: chain 'H' and resid 281 through 283 Processing sheet with id=AC9, first strand: chain 'I' and resid 144 through 146 Processing sheet with id=AD1, first strand: chain 'I' and resid 281 through 283 478 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3668 1.33 - 1.45: 3744 1.45 - 1.57: 9633 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17115 Sorted by residual: bond pdb=" N VAL G 25 " pdb=" CA VAL G 25 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.04e-02 9.25e+03 1.53e+01 bond pdb=" N ILE I 147 " pdb=" CA ILE I 147 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.30e-03 1.16e+04 1.52e+01 bond pdb=" CA PRO D 91 " pdb=" C PRO D 91 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.51e+01 bond pdb=" N ILE D 147 " pdb=" CA ILE D 147 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.50e+01 bond pdb=" N VAL I 25 " pdb=" CA VAL I 25 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.48e+01 ... (remaining 17110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 17384 1.55 - 3.11: 5320 3.11 - 4.66: 585 4.66 - 6.21: 40 6.21 - 7.76: 2 Bond angle restraints: 23331 Sorted by residual: angle pdb=" N ILE I 147 " pdb=" CA ILE I 147 " pdb=" C ILE I 147 " ideal model delta sigma weight residual 113.20 108.08 5.12 9.60e-01 1.09e+00 2.84e+01 angle pdb=" N ILE H 147 " pdb=" CA ILE H 147 " pdb=" C ILE H 147 " ideal model delta sigma weight residual 112.43 107.61 4.82 9.20e-01 1.18e+00 2.74e+01 angle pdb=" N PRO B 292 " pdb=" CA PRO B 292 " pdb=" C PRO B 292 " ideal model delta sigma weight residual 110.80 118.56 -7.76 1.51e+00 4.39e-01 2.64e+01 angle pdb=" N ILE A 147 " pdb=" CA ILE A 147 " pdb=" C ILE A 147 " ideal model delta sigma weight residual 112.90 108.13 4.77 9.60e-01 1.09e+00 2.46e+01 angle pdb=" N ILE D 147 " pdb=" CA ILE D 147 " pdb=" C ILE D 147 " ideal model delta sigma weight residual 113.47 108.49 4.98 1.01e+00 9.80e-01 2.43e+01 ... (remaining 23326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 9068 17.43 - 34.85: 827 34.85 - 52.28: 101 52.28 - 69.71: 124 69.71 - 87.13: 2 Dihedral angle restraints: 10122 sinusoidal: 3759 harmonic: 6363 Sorted by residual: dihedral pdb=" CD ARG D 207 " pdb=" NE ARG D 207 " pdb=" CZ ARG D 207 " pdb=" NH1 ARG D 207 " ideal model delta sinusoidal sigma weight residual 0.00 -34.56 34.56 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CD ARG C 77 " pdb=" NE ARG C 77 " pdb=" CZ ARG C 77 " pdb=" NH1 ARG C 77 " ideal model delta sinusoidal sigma weight residual 0.00 31.10 -31.10 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CD ARG D 232 " pdb=" NE ARG D 232 " pdb=" CZ ARG D 232 " pdb=" NH1 ARG D 232 " ideal model delta sinusoidal sigma weight residual 0.00 -29.91 29.91 1 1.00e+01 1.00e-02 1.28e+01 ... (remaining 10119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 967 0.048 - 0.097: 839 0.097 - 0.145: 552 0.145 - 0.194: 281 0.194 - 0.242: 42 Chirality restraints: 2681 Sorted by residual: chirality pdb=" CA ILE H 36 " pdb=" N ILE H 36 " pdb=" C ILE H 36 " pdb=" CB ILE H 36 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE H 264 " pdb=" N ILE H 264 " pdb=" C ILE H 264 " pdb=" CB ILE H 264 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL C 316 " pdb=" N VAL C 316 " pdb=" C VAL C 316 " pdb=" CB VAL C 316 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2678 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 207 " 0.606 9.50e-02 1.11e+02 2.71e-01 4.50e+01 pdb=" NE ARG D 207 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 207 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 207 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 207 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 77 " -0.561 9.50e-02 1.11e+02 2.52e-01 3.87e+01 pdb=" NE ARG C 77 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 77 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 77 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 77 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 232 " -0.525 9.50e-02 1.11e+02 2.35e-01 3.39e+01 pdb=" NE ARG D 232 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 232 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 232 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 232 " -0.016 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3677 2.81 - 3.33: 17418 3.33 - 3.85: 30570 3.85 - 4.38: 36149 4.38 - 4.90: 57481 Nonbonded interactions: 145295 Sorted by model distance: nonbonded pdb=" OD2 ASP D 46 " pdb=" OH TYR H 66 " model vdw 2.285 3.040 nonbonded pdb=" O GLY D 34 " pdb=" N GLY D 241 " model vdw 2.347 3.120 nonbonded pdb=" OD1 ASP G 169 " pdb=" OG SER I 181 " model vdw 2.367 3.040 nonbonded pdb=" OG SER C 181 " pdb=" OD1 ASP D 169 " model vdw 2.378 3.040 nonbonded pdb=" O ALA C 227 " pdb=" OG1 THR C 230 " model vdw 2.396 3.040 ... (remaining 145290 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.012 0.041 17115 Z= 0.919 Angle : 1.365 7.763 23331 Z= 1.059 Chirality : 0.091 0.242 2681 Planarity : 0.020 0.271 3087 Dihedral : 15.021 87.135 6048 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.72 % Allowed : 10.54 % Favored : 84.74 % 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: -1.89 (0.16), residues: 2226 helix: -0.66 (0.20), residues: 574 sheet: -1.13 (0.22), residues: 522 loop : -1.58 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 33 TYR 0.017 0.002 TYR H 283 PHE 0.014 0.002 PHE A 9 TRP 0.018 0.002 TRP C 12 HIS 0.007 0.002 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.01202 (17115) covalent geometry : angle 1.36461 (23331) hydrogen bonds : bond 0.19620 ( 478) hydrogen bonds : angle 7.28806 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 453 time to evaluate : 0.496 Fit side-chains REVERT: A 16 THR cc_start: 0.9174 (p) cc_final: 0.8915 (p) REVERT: A 135 LYS cc_start: 0.8879 (tttp) cc_final: 0.8559 (tttp) REVERT: A 165 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.6006 (mmt180) REVERT: A 284 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6928 (p0) REVERT: A 285 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7414 (tt) REVERT: C 213 ARG cc_start: 0.8505 (mtt90) cc_final: 0.8296 (mtt180) REVERT: D 24 GLN cc_start: 0.7804 (pt0) cc_final: 0.7265 (tm-30) REVERT: D 123 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8058 (mmt) REVERT: D 124 GLN cc_start: 0.8518 (tt0) cc_final: 0.8253 (tt0) REVERT: D 250 ASP cc_start: 0.7266 (p0) cc_final: 0.7036 (p0) REVERT: G 126 MET cc_start: 0.8925 (mtm) cc_final: 0.8721 (mtm) REVERT: G 164 GLN cc_start: 0.7382 (mt0) cc_final: 0.7115 (mt0) REVERT: H 135 LYS cc_start: 0.8377 (tttp) cc_final: 0.8176 (ttpp) REVERT: H 165 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8314 (mtp85) outliers start: 82 outliers final: 16 residues processed: 497 average time/residue: 0.5373 time to fit residues: 300.6681 Evaluate side-chains 284 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 10 ASN A 24 GLN A 275 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 197 GLN B 247 GLN C 7 GLN C 24 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 164 GLN C 175 GLN C 269 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN G 24 GLN G 108 GLN G 275 ASN H 164 GLN I 24 GLN I 43 ASN I 82 ASN I 94 ASN I 164 GLN I 180 HIS I 190 ASN I 247 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134664 restraints weight = 21037.008| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.41 r_work: 0.3366 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17115 Z= 0.125 Angle : 0.540 8.900 23331 Z= 0.284 Chirality : 0.042 0.155 2681 Planarity : 0.004 0.042 3087 Dihedral : 5.115 58.791 2418 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.90 % Allowed : 18.09 % Favored : 77.02 % 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: -0.57 (0.17), residues: 2226 helix: 1.14 (0.23), residues: 573 sheet: -0.64 (0.23), residues: 527 loop : -1.02 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 207 TYR 0.010 0.001 TYR B 274 PHE 0.022 0.002 PHE A 185 TRP 0.020 0.001 TRP H 12 HIS 0.008 0.002 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00261 (17115) covalent geometry : angle 0.54046 (23331) hydrogen bonds : bond 0.05424 ( 478) hydrogen bonds : angle 4.95611 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 280 time to evaluate : 0.690 Fit side-chains REVERT: A 101 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7677 (mmp-170) REVERT: A 135 LYS cc_start: 0.8946 (tttp) cc_final: 0.8725 (ttpp) REVERT: A 165 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.6385 (mmt180) REVERT: A 173 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: A 187 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 285 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 189 ASP cc_start: 0.8492 (t70) cc_final: 0.8104 (t0) REVERT: C 11 ASP cc_start: 0.7237 (m-30) cc_final: 0.6684 (m-30) REVERT: C 57 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: C 101 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7290 (mmp80) REVERT: C 121 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: C 231 LEU cc_start: 0.8894 (tp) cc_final: 0.8615 (tp) REVERT: D 21 LEU cc_start: 0.7752 (tp) cc_final: 0.7445 (tp) REVERT: D 24 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: D 123 MET cc_start: 0.8061 (mmp) cc_final: 0.7818 (mmm) REVERT: D 190 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7896 (t0) REVERT: D 250 ASP cc_start: 0.7084 (p0) cc_final: 0.6771 (p0) REVERT: D 251 PHE cc_start: 0.7995 (t80) cc_final: 0.7671 (t80) REVERT: G 126 MET cc_start: 0.8985 (mtm) cc_final: 0.8483 (mtm) REVERT: H 70 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5868 (m-30) REVERT: H 135 LYS cc_start: 0.8414 (tttp) cc_final: 0.8014 (tttp) REVERT: I 167 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7821 (t80) outliers start: 85 outliers final: 26 residues processed: 337 average time/residue: 0.4677 time to fit residues: 180.5434 Evaluate side-chains 273 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 66 optimal weight: 0.0980 chunk 163 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 269 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 108 GLN G 124 GLN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN I 233 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109490 restraints weight = 21460.322| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.29 r_work: 0.3051 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17115 Z= 0.246 Angle : 0.687 9.854 23331 Z= 0.361 Chirality : 0.048 0.189 2681 Planarity : 0.005 0.061 3087 Dihedral : 5.601 66.232 2400 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.16 % Allowed : 17.34 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2226 helix: 0.96 (0.22), residues: 579 sheet: -0.63 (0.21), residues: 529 loop : -0.93 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.021 0.003 TYR A 66 PHE 0.024 0.003 PHE B 251 TRP 0.047 0.003 TRP B 53 HIS 0.010 0.002 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00588 (17115) covalent geometry : angle 0.68737 (23331) hydrogen bonds : bond 0.06806 ( 478) hydrogen bonds : angle 4.80969 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 259 time to evaluate : 0.675 Fit side-chains REVERT: A 24 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8311 (tm-30) REVERT: A 68 ASN cc_start: 0.8251 (p0) cc_final: 0.7836 (p0) REVERT: A 101 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8330 (mmp-170) REVERT: A 105 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8607 (mtmt) REVERT: A 173 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: A 229 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 271 GLU cc_start: 0.8761 (pt0) cc_final: 0.8551 (pt0) REVERT: B 189 ASP cc_start: 0.8599 (t70) cc_final: 0.8186 (t0) REVERT: B 236 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8637 (mt) REVERT: C 11 ASP cc_start: 0.7740 (m-30) cc_final: 0.7314 (m-30) REVERT: C 57 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: C 82 ASN cc_start: 0.7613 (m-40) cc_final: 0.7406 (m-40) REVERT: C 101 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7859 (mmp80) REVERT: C 121 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: C 231 LEU cc_start: 0.8880 (tp) cc_final: 0.8584 (tp) REVERT: C 259 THR cc_start: 0.8744 (p) cc_final: 0.8321 (t) REVERT: D 24 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: D 108 GLN cc_start: 0.7799 (pp30) cc_final: 0.7591 (pp30) REVERT: D 123 MET cc_start: 0.8159 (mmp) cc_final: 0.7893 (mmm) REVERT: D 190 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8311 (t0) REVERT: D 250 ASP cc_start: 0.7878 (p0) cc_final: 0.7500 (p0) REVERT: G 17 MET cc_start: 0.7761 (pp-130) cc_final: 0.7557 (pp-130) REVERT: G 49 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: G 173 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7477 (t0) REVERT: G 276 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8820 (tp) REVERT: H 61 ARG cc_start: 0.7721 (ptt90) cc_final: 0.7342 (ptt-90) REVERT: H 70 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.6199 (m-30) REVERT: H 135 LYS cc_start: 0.8360 (tttp) cc_final: 0.7831 (tttp) REVERT: H 155 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.4914 (mmt) REVERT: H 189 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8080 (t0) REVERT: H 192 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8378 (mt) REVERT: H 199 TYR cc_start: 0.8829 (m-80) cc_final: 0.8587 (m-80) REVERT: H 305 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7193 (tptm) REVERT: I 167 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8055 (t80) REVERT: I 170 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7643 (mmm-85) outliers start: 107 outliers final: 55 residues processed: 335 average time/residue: 0.4884 time to fit residues: 187.3706 Evaluate side-chains 303 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 229 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 305 LYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 135 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 78 optimal weight: 0.4980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 197 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.134379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113525 restraints weight = 21262.741| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.25 r_work: 0.3148 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17115 Z= 0.115 Angle : 0.514 7.574 23331 Z= 0.267 Chirality : 0.042 0.142 2681 Planarity : 0.004 0.048 3087 Dihedral : 4.927 59.373 2397 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.61 % Allowed : 18.66 % Favored : 76.73 % 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: -0.40 (0.17), residues: 2226 helix: 1.06 (0.22), residues: 580 sheet: -0.45 (0.22), residues: 521 loop : -0.83 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.014 0.001 TYR I 199 PHE 0.012 0.001 PHE G 211 TRP 0.010 0.001 TRP B 53 HIS 0.005 0.001 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00255 (17115) covalent geometry : angle 0.51401 (23331) hydrogen bonds : bond 0.04909 ( 478) hydrogen bonds : angle 4.33623 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 68 ASN cc_start: 0.8032 (p0) cc_final: 0.7602 (p0) REVERT: A 70 ASP cc_start: 0.8277 (m-30) cc_final: 0.7997 (m-30) REVERT: A 101 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8394 (mmp-170) REVERT: A 229 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 17 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6841 (pp-130) REVERT: B 189 ASP cc_start: 0.8496 (t70) cc_final: 0.8072 (t0) REVERT: B 252 ASP cc_start: 0.8712 (m-30) cc_final: 0.8485 (m-30) REVERT: C 11 ASP cc_start: 0.7852 (m-30) cc_final: 0.7534 (m-30) REVERT: C 101 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8025 (mmp80) REVERT: C 121 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: C 167 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: C 231 LEU cc_start: 0.8843 (tp) cc_final: 0.8564 (tp) REVERT: C 259 THR cc_start: 0.8702 (p) cc_final: 0.8436 (p) REVERT: D 21 LEU cc_start: 0.7708 (tp) cc_final: 0.7487 (tp) REVERT: D 24 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: D 108 GLN cc_start: 0.7821 (pp30) cc_final: 0.7540 (pp30) REVERT: D 123 MET cc_start: 0.8349 (mmp) cc_final: 0.8082 (mmm) REVERT: D 250 ASP cc_start: 0.7706 (p0) cc_final: 0.7403 (p0) REVERT: G 15 LYS cc_start: 0.8688 (mttt) cc_final: 0.8419 (mttt) REVERT: G 17 MET cc_start: 0.7624 (pp-130) cc_final: 0.6999 (pp-130) REVERT: G 22 ASP cc_start: 0.7186 (t0) cc_final: 0.6973 (t70) REVERT: G 173 ASP cc_start: 0.7979 (m-30) cc_final: 0.7346 (t0) REVERT: H 135 LYS cc_start: 0.8309 (tttp) cc_final: 0.7759 (tttp) REVERT: H 147 ILE cc_start: 0.7727 (tt) cc_final: 0.7323 (mm) REVERT: H 155 MET cc_start: 0.5650 (ptm) cc_final: 0.4797 (mmt) REVERT: H 192 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8316 (mt) REVERT: I 167 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8152 (t80) REVERT: I 170 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7455 (mtm-85) REVERT: I 257 ASP cc_start: 0.7186 (m-30) cc_final: 0.6917 (t0) REVERT: I 305 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7784 (tptp) outliers start: 80 outliers final: 28 residues processed: 297 average time/residue: 0.4660 time to fit residues: 158.7740 Evaluate side-chains 258 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 17 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 108 GLN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN I 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107184 restraints weight = 21229.239| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.27 r_work: 0.3022 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17115 Z= 0.200 Angle : 0.596 8.577 23331 Z= 0.309 Chirality : 0.045 0.155 2681 Planarity : 0.004 0.049 3087 Dihedral : 5.344 63.153 2397 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.82 % Allowed : 17.91 % Favored : 76.27 % 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: -0.45 (0.17), residues: 2226 helix: 0.94 (0.22), residues: 578 sheet: -0.41 (0.22), residues: 519 loop : -0.85 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 33 TYR 0.012 0.002 TYR G 14 PHE 0.018 0.002 PHE D 9 TRP 0.021 0.002 TRP B 53 HIS 0.006 0.002 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00475 (17115) covalent geometry : angle 0.59562 (23331) hydrogen bonds : bond 0.05933 ( 478) hydrogen bonds : angle 4.45256 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 222 time to evaluate : 0.611 Fit side-chains REVERT: A 68 ASN cc_start: 0.8212 (p0) cc_final: 0.7768 (p0) REVERT: A 101 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8150 (mmp-170) REVERT: A 105 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: A 229 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 83 THR cc_start: 0.9042 (t) cc_final: 0.8760 (p) REVERT: B 173 ASP cc_start: 0.8580 (m-30) cc_final: 0.8364 (m-30) REVERT: B 189 ASP cc_start: 0.8554 (t70) cc_final: 0.8102 (t0) REVERT: C 11 ASP cc_start: 0.7862 (m-30) cc_final: 0.7528 (m-30) REVERT: C 101 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7892 (mmp80) REVERT: C 121 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: C 231 LEU cc_start: 0.8800 (tp) cc_final: 0.8510 (tp) REVERT: D 11 ASP cc_start: 0.6567 (t70) cc_final: 0.6269 (t0) REVERT: D 21 LEU cc_start: 0.7730 (tp) cc_final: 0.7491 (tp) REVERT: D 24 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: D 108 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: D 123 MET cc_start: 0.8105 (mmp) cc_final: 0.7868 (mmm) REVERT: D 190 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8201 (t0) REVERT: D 250 ASP cc_start: 0.7890 (p0) cc_final: 0.7573 (p0) REVERT: G 15 LYS cc_start: 0.8761 (mttt) cc_final: 0.8488 (mttt) REVERT: H 61 ARG cc_start: 0.7888 (ptt90) cc_final: 0.7634 (ppt-90) REVERT: H 135 LYS cc_start: 0.8284 (tttp) cc_final: 0.7743 (tttp) REVERT: H 147 ILE cc_start: 0.7825 (tt) cc_final: 0.7450 (mm) REVERT: H 155 MET cc_start: 0.5743 (ptm) cc_final: 0.4854 (mmt) REVERT: H 189 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8307 (t0) REVERT: H 192 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8473 (mt) REVERT: H 204 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.7992 (m) REVERT: I 167 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8014 (t80) REVERT: I 246 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 101 outliers final: 51 residues processed: 290 average time/residue: 0.4583 time to fit residues: 153.0847 Evaluate side-chains 271 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN H 190 ASN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106840 restraints weight = 21175.610| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.21 r_work: 0.3004 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17115 Z= 0.190 Angle : 0.580 9.009 23331 Z= 0.301 Chirality : 0.044 0.150 2681 Planarity : 0.004 0.053 3087 Dihedral : 5.379 65.835 2397 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.36 % Allowed : 18.84 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2226 helix: 0.87 (0.22), residues: 580 sheet: -0.39 (0.22), residues: 519 loop : -0.86 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 158 TYR 0.011 0.002 TYR I 199 PHE 0.014 0.002 PHE G 211 TRP 0.012 0.002 TRP B 53 HIS 0.005 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00449 (17115) covalent geometry : angle 0.57986 (23331) hydrogen bonds : bond 0.05719 ( 478) hydrogen bonds : angle 4.40120 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 216 time to evaluate : 0.671 Fit side-chains REVERT: A 24 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: A 68 ASN cc_start: 0.8169 (p0) cc_final: 0.7679 (p0) REVERT: A 101 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8318 (mmp-170) REVERT: A 125 ASP cc_start: 0.8802 (t70) cc_final: 0.8556 (t70) REVERT: B 83 THR cc_start: 0.9067 (t) cc_final: 0.8782 (p) REVERT: B 173 ASP cc_start: 0.8591 (m-30) cc_final: 0.8358 (m-30) REVERT: B 189 ASP cc_start: 0.8600 (t70) cc_final: 0.8168 (t0) REVERT: C 11 ASP cc_start: 0.7838 (m-30) cc_final: 0.7577 (m-30) REVERT: C 101 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7948 (mmp80) REVERT: C 121 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: C 167 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: C 196 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: C 231 LEU cc_start: 0.8810 (tp) cc_final: 0.8527 (tp) REVERT: D 11 ASP cc_start: 0.7090 (t70) cc_final: 0.6757 (t0) REVERT: D 21 LEU cc_start: 0.7730 (tp) cc_final: 0.7495 (tp) REVERT: D 24 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: D 108 GLN cc_start: 0.7760 (pp30) cc_final: 0.7533 (pp30) REVERT: D 123 MET cc_start: 0.8163 (mmp) cc_final: 0.7914 (mmm) REVERT: D 169 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6786 (t0) REVERT: D 190 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8215 (t0) REVERT: D 250 ASP cc_start: 0.7784 (p0) cc_final: 0.7447 (p0) REVERT: G 15 LYS cc_start: 0.8783 (mttt) cc_final: 0.8545 (mttt) REVERT: H 61 ARG cc_start: 0.7944 (ptt90) cc_final: 0.7560 (ptt90) REVERT: H 121 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: H 135 LYS cc_start: 0.8313 (tttp) cc_final: 0.7874 (tttp) REVERT: H 147 ILE cc_start: 0.7858 (tt) cc_final: 0.7516 (mm) REVERT: H 155 MET cc_start: 0.5808 (ptm) cc_final: 0.4918 (mmt) REVERT: H 192 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8573 (mt) REVERT: H 204 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.7986 (m) REVERT: I 167 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8037 (t80) REVERT: I 246 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8258 (mt-10) REVERT: I 257 ASP cc_start: 0.8070 (m-30) cc_final: 0.7752 (m-30) REVERT: I 305 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (tptp) outliers start: 93 outliers final: 58 residues processed: 280 average time/residue: 0.4785 time to fit residues: 153.1967 Evaluate side-chains 279 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 207 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 85 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 GLN I 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110169 restraints weight = 20935.618| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.22 r_work: 0.3038 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17115 Z= 0.128 Angle : 0.535 9.375 23331 Z= 0.274 Chirality : 0.042 0.131 2681 Planarity : 0.004 0.049 3087 Dihedral : 5.121 64.112 2397 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.38 % Allowed : 20.16 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2226 helix: 0.96 (0.22), residues: 580 sheet: -0.18 (0.22), residues: 499 loop : -0.84 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.010 0.001 TYR G 199 PHE 0.012 0.001 PHE G 211 TRP 0.011 0.001 TRP A 303 HIS 0.005 0.001 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00291 (17115) covalent geometry : angle 0.53514 (23331) hydrogen bonds : bond 0.04946 ( 478) hydrogen bonds : angle 4.20203 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 223 time to evaluate : 0.669 Fit side-chains REVERT: A 68 ASN cc_start: 0.8073 (p0) cc_final: 0.7589 (p0) REVERT: A 101 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8389 (mmp-170) REVERT: A 105 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8462 (mtmt) REVERT: A 125 ASP cc_start: 0.8746 (t70) cc_final: 0.8486 (t70) REVERT: B 83 THR cc_start: 0.9034 (t) cc_final: 0.8771 (p) REVERT: B 173 ASP cc_start: 0.8587 (m-30) cc_final: 0.8363 (m-30) REVERT: B 189 ASP cc_start: 0.8587 (t70) cc_final: 0.8154 (t0) REVERT: C 78 GLN cc_start: 0.8943 (pt0) cc_final: 0.8732 (pt0) REVERT: C 121 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: C 167 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: D 11 ASP cc_start: 0.7259 (t70) cc_final: 0.6944 (t0) REVERT: D 24 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: D 121 ASP cc_start: 0.7883 (m-30) cc_final: 0.7151 (m-30) REVERT: D 123 MET cc_start: 0.8357 (mmp) cc_final: 0.8136 (mmm) REVERT: D 190 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8179 (t0) REVERT: D 250 ASP cc_start: 0.7754 (p0) cc_final: 0.7418 (p0) REVERT: G 15 LYS cc_start: 0.8786 (mttt) cc_final: 0.8536 (mttt) REVERT: G 173 ASP cc_start: 0.7902 (m-30) cc_final: 0.7253 (t0) REVERT: H 61 ARG cc_start: 0.7933 (ptt90) cc_final: 0.7708 (ppt-90) REVERT: H 135 LYS cc_start: 0.8316 (tttp) cc_final: 0.7771 (tttp) REVERT: H 147 ILE cc_start: 0.7831 (tt) cc_final: 0.7526 (mm) REVERT: H 155 MET cc_start: 0.5606 (ptm) cc_final: 0.4786 (mmt) REVERT: H 192 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8516 (mt) REVERT: H 204 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.7970 (m) REVERT: H 252 ASP cc_start: 0.6979 (t0) cc_final: 0.6479 (m-30) REVERT: I 167 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8190 (t80) REVERT: I 246 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8242 (mt-10) REVERT: I 257 ASP cc_start: 0.8052 (m-30) cc_final: 0.7754 (m-30) REVERT: I 305 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8084 (tptp) outliers start: 76 outliers final: 51 residues processed: 279 average time/residue: 0.5428 time to fit residues: 171.3154 Evaluate side-chains 275 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 177 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 160 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 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 = 0.3361 r_free = 0.3361 target = 0.126521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105731 restraints weight = 21200.661| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.20 r_work: 0.2986 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17115 Z= 0.207 Angle : 0.610 9.595 23331 Z= 0.314 Chirality : 0.045 0.143 2681 Planarity : 0.004 0.050 3087 Dihedral : 5.463 68.285 2396 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.95 % Allowed : 19.99 % Favored : 75.06 % 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: -0.43 (0.17), residues: 2226 helix: 0.86 (0.22), residues: 580 sheet: -0.21 (0.22), residues: 499 loop : -0.89 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.012 0.002 TYR I 199 PHE 0.015 0.002 PHE G 211 TRP 0.013 0.002 TRP B 53 HIS 0.007 0.002 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00495 (17115) covalent geometry : angle 0.61041 (23331) hydrogen bonds : bond 0.05916 ( 478) hydrogen bonds : angle 4.38699 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 215 time to evaluate : 0.680 Fit side-chains REVERT: A 68 ASN cc_start: 0.8015 (p0) cc_final: 0.7677 (p0) REVERT: A 101 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8248 (mmp-170) REVERT: A 105 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8551 (mtmt) REVERT: A 125 ASP cc_start: 0.8770 (t70) cc_final: 0.8509 (t70) REVERT: A 284 ASP cc_start: 0.7495 (p0) cc_final: 0.7233 (p0) REVERT: B 83 THR cc_start: 0.9092 (t) cc_final: 0.8825 (p) REVERT: B 173 ASP cc_start: 0.8612 (m-30) cc_final: 0.8392 (m-30) REVERT: B 189 ASP cc_start: 0.8600 (t70) cc_final: 0.8187 (t0) REVERT: C 78 GLN cc_start: 0.8957 (pt0) cc_final: 0.8745 (pt0) REVERT: C 104 GLN cc_start: 0.6977 (mt0) cc_final: 0.6676 (mm110) REVERT: C 121 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: C 167 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: D 24 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: D 70 ASP cc_start: 0.7953 (m-30) cc_final: 0.7374 (m-30) REVERT: D 190 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8252 (t0) REVERT: D 250 ASP cc_start: 0.7788 (p0) cc_final: 0.7446 (p0) REVERT: G 15 LYS cc_start: 0.8842 (mttt) cc_final: 0.8589 (mttt) REVERT: H 61 ARG cc_start: 0.8057 (ptt90) cc_final: 0.7667 (ptt90) REVERT: H 121 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: H 135 LYS cc_start: 0.8319 (tttp) cc_final: 0.7880 (tttp) REVERT: H 147 ILE cc_start: 0.7941 (tt) cc_final: 0.7632 (mm) REVERT: H 155 MET cc_start: 0.5635 (ptm) cc_final: 0.4745 (mmt) REVERT: H 192 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8601 (mt) REVERT: H 252 ASP cc_start: 0.6996 (t0) cc_final: 0.6470 (m-30) REVERT: I 167 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8106 (t80) REVERT: I 257 ASP cc_start: 0.8177 (m-30) cc_final: 0.7869 (m-30) outliers start: 86 outliers final: 63 residues processed: 281 average time/residue: 0.5443 time to fit residues: 173.1121 Evaluate side-chains 278 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 206 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 167 PHE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 163 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 66 optimal weight: 0.0020 chunk 137 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN H 190 ASN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN I 190 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110344 restraints weight = 21036.664| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.27 r_work: 0.3047 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17115 Z= 0.105 Angle : 0.520 10.213 23331 Z= 0.267 Chirality : 0.041 0.128 2681 Planarity : 0.004 0.049 3087 Dihedral : 4.950 63.447 2396 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.74 % Allowed : 21.14 % Favored : 75.12 % 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: -0.24 (0.17), residues: 2226 helix: 0.99 (0.22), residues: 580 sheet: -0.10 (0.22), residues: 499 loop : -0.74 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 33 TYR 0.015 0.001 TYR G 199 PHE 0.011 0.001 PHE G 211 TRP 0.010 0.001 TRP A 303 HIS 0.004 0.001 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00231 (17115) covalent geometry : angle 0.51961 (23331) hydrogen bonds : bond 0.04379 ( 478) hydrogen bonds : angle 4.06996 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.663 Fit side-chains REVERT: A 68 ASN cc_start: 0.8021 (p0) cc_final: 0.7562 (p0) REVERT: A 101 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8332 (mmp-170) REVERT: A 125 ASP cc_start: 0.8740 (t70) cc_final: 0.8450 (t70) REVERT: A 284 ASP cc_start: 0.7323 (p0) cc_final: 0.7015 (p0) REVERT: A 290 LYS cc_start: 0.6596 (mttp) cc_final: 0.6337 (mttp) REVERT: B 173 ASP cc_start: 0.8613 (m-30) cc_final: 0.8379 (m-30) REVERT: B 189 ASP cc_start: 0.8551 (t70) cc_final: 0.8153 (t0) REVERT: C 104 GLN cc_start: 0.7198 (mt0) cc_final: 0.6849 (mm-40) REVERT: C 121 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: C 167 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: D 24 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: D 70 ASP cc_start: 0.7971 (m-30) cc_final: 0.7672 (m-30) REVERT: D 121 ASP cc_start: 0.8010 (m-30) cc_final: 0.7705 (m-30) REVERT: D 123 MET cc_start: 0.8375 (tpp) cc_final: 0.7815 (mmm) REVERT: D 250 ASP cc_start: 0.7747 (p0) cc_final: 0.7415 (p0) REVERT: G 15 LYS cc_start: 0.8889 (mttt) cc_final: 0.8620 (mttt) REVERT: G 17 MET cc_start: 0.7737 (ppp) cc_final: 0.7155 (mpm) REVERT: G 173 ASP cc_start: 0.7939 (m-30) cc_final: 0.7281 (t0) REVERT: H 61 ARG cc_start: 0.8045 (ptt90) cc_final: 0.7802 (ppt-90) REVERT: H 85 LYS cc_start: 0.7589 (ttpt) cc_final: 0.7268 (ttpt) REVERT: H 99 MET cc_start: 0.6954 (ptt) cc_final: 0.6658 (ptt) REVERT: H 135 LYS cc_start: 0.8358 (tttp) cc_final: 0.7817 (tttp) REVERT: H 147 ILE cc_start: 0.7853 (tt) cc_final: 0.7532 (mm) REVERT: H 155 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4611 (mmt) REVERT: H 192 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8589 (mt) REVERT: H 252 ASP cc_start: 0.7032 (t0) cc_final: 0.6523 (m-30) REVERT: I 257 ASP cc_start: 0.8116 (m-30) cc_final: 0.7817 (m-30) REVERT: I 305 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7878 (tptp) outliers start: 65 outliers final: 37 residues processed: 274 average time/residue: 0.4746 time to fit residues: 148.2176 Evaluate side-chains 257 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 117 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** H 248 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 = 0.3401 r_free = 0.3401 target = 0.129618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108094 restraints weight = 21015.315| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.28 r_work: 0.3015 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17115 Z= 0.135 Angle : 0.545 10.120 23331 Z= 0.278 Chirality : 0.042 0.167 2681 Planarity : 0.004 0.049 3087 Dihedral : 4.998 62.141 2396 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.65 % Allowed : 22.35 % Favored : 75.00 % 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: -0.20 (0.18), residues: 2226 helix: 1.02 (0.22), residues: 580 sheet: -0.06 (0.22), residues: 499 loop : -0.73 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 33 TYR 0.019 0.001 TYR I 199 PHE 0.009 0.001 PHE G 211 TRP 0.007 0.001 TRP C 12 HIS 0.004 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00313 (17115) covalent geometry : angle 0.54528 (23331) hydrogen bonds : bond 0.04789 ( 478) hydrogen bonds : angle 4.09746 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.558 Fit side-chains REVERT: A 68 ASN cc_start: 0.8070 (p0) cc_final: 0.7647 (p0) REVERT: A 101 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8337 (mmp-170) REVERT: A 125 ASP cc_start: 0.8753 (t70) cc_final: 0.8468 (t70) REVERT: A 290 LYS cc_start: 0.6230 (mttp) cc_final: 0.5922 (mttp) REVERT: B 189 ASP cc_start: 0.8627 (t70) cc_final: 0.8218 (t0) REVERT: C 78 GLN cc_start: 0.8964 (pt0) cc_final: 0.8742 (pt0) REVERT: C 104 GLN cc_start: 0.7204 (mt0) cc_final: 0.6862 (mm-40) REVERT: C 121 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: C 167 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: D 24 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: D 70 ASP cc_start: 0.8046 (m-30) cc_final: 0.7762 (m-30) REVERT: D 121 ASP cc_start: 0.7992 (m-30) cc_final: 0.7672 (m-30) REVERT: D 123 MET cc_start: 0.8396 (tpp) cc_final: 0.7833 (mmm) REVERT: D 250 ASP cc_start: 0.7760 (p0) cc_final: 0.7423 (p0) REVERT: G 15 LYS cc_start: 0.8911 (mttt) cc_final: 0.8644 (mttt) REVERT: G 17 MET cc_start: 0.7751 (ppp) cc_final: 0.7169 (mpm) REVERT: G 173 ASP cc_start: 0.7965 (m-30) cc_final: 0.7360 (t0) REVERT: H 61 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7825 (ppt-90) REVERT: H 135 LYS cc_start: 0.8346 (tttp) cc_final: 0.7821 (tttp) REVERT: H 147 ILE cc_start: 0.7854 (tt) cc_final: 0.7554 (mm) REVERT: H 155 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4582 (mmt) REVERT: I 257 ASP cc_start: 0.8218 (m-30) cc_final: 0.7942 (m-30) REVERT: I 305 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8150 (tptp) outliers start: 46 outliers final: 39 residues processed: 252 average time/residue: 0.5238 time to fit residues: 149.3207 Evaluate side-chains 256 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 155 MET Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 319 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 92 optimal weight: 0.0000 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN H 57 GLN ** H 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110730 restraints weight = 20906.069| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.18 r_work: 0.3062 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17115 Z= 0.110 Angle : 0.527 12.885 23331 Z= 0.268 Chirality : 0.041 0.185 2681 Planarity : 0.004 0.053 3087 Dihedral : 4.845 59.673 2396 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.05 % Allowed : 22.12 % Favored : 74.83 % 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: -0.12 (0.18), residues: 2226 helix: 1.07 (0.22), residues: 581 sheet: 0.00 (0.23), residues: 499 loop : -0.67 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 33 TYR 0.021 0.001 TYR I 199 PHE 0.008 0.001 PHE H 52 TRP 0.007 0.001 TRP C 12 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00248 (17115) covalent geometry : angle 0.52724 (23331) hydrogen bonds : bond 0.04360 ( 478) hydrogen bonds : angle 4.00324 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7028.38 seconds wall clock time: 120 minutes 15.85 seconds (7215.85 seconds total)