Starting phenix.real_space_refine on Tue Feb 3 23:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.map" model { file = "/net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lfl_63050/02_2026/9lfl_63050.cif" } resolution = 3.73 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= 0.008 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 44 5.16 5 C 4820 2.51 5 N 1289 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 7710 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1154 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "B" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1676 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Chain: "D" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1696 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 208} Chain: "E" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1549 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 195} Time building chain proxies: 1.97, per 1000 atoms: 0.26 Number of scatterers: 7710 At special positions: 0 Unit cell: (76.504, 102.704, 173.968, 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 44 16.00 O 1557 8.00 N 1289 7.00 C 4820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 31 " distance=2.04 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 45 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 141 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 361.0 milliseconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 23 sheets defined 6.8% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.604A pdb=" N LYS B 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.741A pdb=" N THR B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.574A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 128 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 128 through 134 Processing helix chain 'D' and resid 190 through 197 removed outlier: 4.054A pdb=" N LYS D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 131 removed outlier: 3.571A pdb=" N SER E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.840A pdb=" N THR E 188 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.912A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 12 removed outlier: 5.625A pdb=" N GLU B 10 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.685A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR B 182 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.685A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR B 182 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 157 through 160 removed outlier: 4.245A pdb=" N TYR B 200 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 21 removed outlier: 3.982A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.407A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.768A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.931A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN D 5 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 34 through 38 removed outlier: 6.352A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (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 121 through 125 removed outlier: 5.169A pdb=" N SER D 138 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU D 188 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 140 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU D 186 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU D 142 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER D 184 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN D 144 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU D 182 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 179 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 160 through 162 removed outlier: 4.513A pdb=" N TRP D 155 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR D 199 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS D 201 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 212 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.714A pdb=" N THR E 5 " --> pdb=" O THR E 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.169A pdb=" N MET E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 46 through 47 removed outlier: 3.812A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 117 through 121 removed outlier: 4.093A pdb=" N GLY E 136 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 177 " --> pdb=" O CYS E 137 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 173 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 117 through 121 removed outlier: 4.093A pdb=" N GLY E 136 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E 177 " --> pdb=" O CYS E 137 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 173 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 148 through 151 removed outlier: 4.178A pdb=" N TYR E 191 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 204 " --> pdb=" O VAL E 195 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2459 1.35 - 1.47: 2009 1.47 - 1.59: 3375 1.59 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 7895 Sorted by residual: bond pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 1.503 1.345 0.158 3.40e-02 8.65e+02 2.15e+01 bond pdb=" CA ASP B 107 " pdb=" C ASP B 107 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.41e-02 5.03e+03 6.51e+00 bond pdb=" C ARG A 77 " pdb=" N CYS A 78 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.35e-02 5.49e+03 2.80e+00 bond pdb=" CA GLY E 69 " pdb=" C GLY E 69 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.39e+00 bond pdb=" CA CYS A 88 " pdb=" CB CYS A 88 " ideal model delta sigma weight residual 1.528 1.566 -0.038 2.61e-02 1.47e+03 2.14e+00 ... (remaining 7890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 10436 2.34 - 4.68: 275 4.68 - 7.02: 31 7.02 - 9.36: 7 9.36 - 11.70: 3 Bond angle restraints: 10752 Sorted by residual: angle pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 112.00 100.80 11.20 1.40e+00 5.10e-01 6.39e+01 angle pdb=" N PRO A 144 " pdb=" CD PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 103.20 91.50 11.70 1.50e+00 4.44e-01 6.09e+01 angle pdb=" N ALA C 84 " pdb=" CA ALA C 84 " pdb=" C ALA C 84 " ideal model delta sigma weight residual 107.73 113.82 -6.09 1.34e+00 5.57e-01 2.07e+01 angle pdb=" CA PRO A 144 " pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 104.50 96.38 8.12 1.90e+00 2.77e-01 1.83e+01 angle pdb=" C HIS D 35 " pdb=" N TRP D 36 " pdb=" CA TRP D 36 " ideal model delta sigma weight residual 122.59 115.92 6.67 1.57e+00 4.06e-01 1.80e+01 ... (remaining 10747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4164 17.95 - 35.90: 458 35.90 - 53.85: 114 53.85 - 71.80: 24 71.80 - 89.75: 9 Dihedral angle restraints: 4769 sinusoidal: 1822 harmonic: 2947 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual -180.00 -123.68 -56.32 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CB CYS A 32 " pdb=" SG CYS A 32 " pdb=" SG CYS A 45 " pdb=" CB CYS A 45 " ideal model delta sinusoidal sigma weight residual -86.00 -160.22 74.22 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 112 " pdb=" CB CYS A 112 " ideal model delta sinusoidal sigma weight residual -86.00 -156.60 70.60 1 1.00e+01 1.00e-02 6.41e+01 ... (remaining 4766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 995 0.056 - 0.111: 189 0.111 - 0.167: 28 0.167 - 0.222: 1 0.222 - 0.278: 1 Chirality restraints: 1214 Sorted by residual: chirality pdb=" CG LEU D 81 " pdb=" CB LEU D 81 " pdb=" CD1 LEU D 81 " pdb=" CD2 LEU D 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA TYR C 140 " pdb=" N TYR C 140 " pdb=" C TYR C 140 " pdb=" CB TYR C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CG LEU B 45 " pdb=" CB LEU B 45 " pdb=" CD1 LEU B 45 " pdb=" CD2 LEU B 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1211 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " 0.028 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP D 36 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " 0.085 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO A 144 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " 0.018 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR A 103 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.001 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 116 2.59 - 3.17: 6799 3.17 - 3.75: 12743 3.75 - 4.32: 17057 4.32 - 4.90: 27419 Nonbonded interactions: 64134 Sorted by model distance: nonbonded pdb=" O SER C 30 " pdb=" OH TYR C 71 " model vdw 2.015 3.040 nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.106 3.040 nonbonded pdb=" O TYR D 199 " pdb=" OG SER D 215 " model vdw 2.119 3.040 nonbonded pdb=" OG SER D 128 " pdb=" O PRO E 120 " model vdw 2.139 3.040 nonbonded pdb=" OG1 THR A 60 " pdb=" O LEU A 72 " model vdw 2.147 3.040 ... (remaining 64129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 7913 Z= 0.198 Angle : 0.895 11.704 10788 Z= 0.513 Chirality : 0.046 0.278 1214 Planarity : 0.007 0.121 1373 Dihedral : 16.055 89.751 2825 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.87 % Favored : 89.73 % Rotamer: Outliers : 0.34 % Allowed : 26.11 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.27), residues: 1003 helix: -1.51 (0.76), residues: 38 sheet: -0.68 (0.27), residues: 372 loop : -1.88 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 85 TYR 0.036 0.003 TYR A 103 PHE 0.024 0.002 PHE D 123 TRP 0.089 0.004 TRP D 36 HIS 0.014 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 7895) covalent geometry : angle 0.89264 (10752) SS BOND : bond 0.00264 ( 18) SS BOND : angle 1.46457 ( 36) hydrogen bonds : bond 0.28779 ( 197) hydrogen bonds : angle 11.94915 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 LEU cc_start: 0.6994 (mt) cc_final: 0.6644 (mt) REVERT: D 33 TYR cc_start: 0.4430 (m-10) cc_final: 0.4218 (m-80) REVERT: D 81 LEU cc_start: 0.7739 (tp) cc_final: 0.6332 (tp) REVERT: D 95 TYR cc_start: 0.4753 (m-80) cc_final: 0.4303 (m-80) REVERT: E 90 HIS cc_start: 0.6335 (t70) cc_final: 0.5969 (t70) REVERT: E 98 THR cc_start: 0.5797 (m) cc_final: 0.5161 (p) REVERT: E 181 VAL cc_start: 0.6768 (m) cc_final: 0.6561 (m) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 0.0959 time to fit residues: 19.9066 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 29 GLN A 39 GLN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 79 GLN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 145 ASN D 173 GLN E 38 GLN E 54 ASN E 197 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.132886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.106830 restraints weight = 35042.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.110426 restraints weight = 19509.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.113006 restraints weight = 12933.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.114499 restraints weight = 9624.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.115819 restraints weight = 7877.989| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7913 Z= 0.146 Angle : 0.743 9.366 10788 Z= 0.389 Chirality : 0.045 0.194 1214 Planarity : 0.006 0.070 1373 Dihedral : 5.987 50.296 1088 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.67 % Favored : 91.13 % Rotamer: Outliers : 3.63 % Allowed : 24.52 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.11 % 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: -1.84 (0.27), residues: 1003 helix: -1.42 (0.71), residues: 44 sheet: -0.45 (0.27), residues: 374 loop : -1.78 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.035 0.003 TYR E 72 PHE 0.012 0.002 PHE D 123 TRP 0.057 0.003 TRP D 36 HIS 0.008 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7895) covalent geometry : angle 0.74092 (10752) SS BOND : bond 0.00379 ( 18) SS BOND : angle 1.20302 ( 36) hydrogen bonds : bond 0.04454 ( 197) hydrogen bonds : angle 8.20566 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7538 (m) cc_final: 0.7255 (t) REVERT: B 83 LEU cc_start: 0.6387 (tp) cc_final: 0.5550 (tp) REVERT: C 83 LEU cc_start: 0.7800 (mt) cc_final: 0.7524 (mt) REVERT: C 86 TYR cc_start: 0.8451 (m-80) cc_final: 0.8152 (m-80) REVERT: C 92 TYR cc_start: 0.8030 (t80) cc_final: 0.7819 (t80) REVERT: D 29 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6203 (tt) REVERT: D 81 LEU cc_start: 0.8601 (tp) cc_final: 0.7511 (tp) REVERT: D 159 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7695 (t0) REVERT: E 18 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7618 (mmt90) REVERT: E 34 LEU cc_start: 0.5822 (pt) cc_final: 0.5162 (pt) REVERT: E 76 ILE cc_start: 0.7891 (mp) cc_final: 0.7606 (mm) REVERT: E 90 HIS cc_start: 0.7507 (t70) cc_final: 0.6651 (t70) REVERT: E 98 THR cc_start: 0.6567 (m) cc_final: 0.5471 (p) REVERT: E 175 LEU cc_start: 0.7607 (tp) cc_final: 0.7308 (tp) outliers start: 32 outliers final: 13 residues processed: 143 average time/residue: 0.0990 time to fit residues: 19.0767 Evaluate side-chains 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 109 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.133000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.106903 restraints weight = 35227.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.110691 restraints weight = 19308.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.113450 restraints weight = 12657.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.115191 restraints weight = 9307.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.116044 restraints weight = 7470.491| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7913 Z= 0.133 Angle : 0.690 8.096 10788 Z= 0.358 Chirality : 0.043 0.151 1214 Planarity : 0.006 0.060 1373 Dihedral : 5.736 44.876 1087 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.68 % Favored : 92.12 % Rotamer: Outliers : 4.20 % Allowed : 23.84 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.11 % 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: -1.68 (0.27), residues: 1003 helix: -1.27 (0.72), residues: 43 sheet: -0.24 (0.29), residues: 352 loop : -1.71 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 142 TYR 0.026 0.002 TYR E 72 PHE 0.010 0.002 PHE C 98 TRP 0.046 0.002 TRP D 36 HIS 0.011 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7895) covalent geometry : angle 0.68851 (10752) SS BOND : bond 0.00369 ( 18) SS BOND : angle 0.98477 ( 36) hydrogen bonds : bond 0.03518 ( 197) hydrogen bonds : angle 7.46595 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8225 (t) cc_final: 0.7851 (p) REVERT: B 90 ASP cc_start: 0.6694 (t0) cc_final: 0.6131 (t0) REVERT: C 83 LEU cc_start: 0.8061 (mt) cc_final: 0.7807 (mt) REVERT: C 86 TYR cc_start: 0.8445 (m-80) cc_final: 0.8207 (m-80) REVERT: C 89 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: D 36 TRP cc_start: 0.7036 (m-10) cc_final: 0.6810 (m-10) REVERT: D 110 LEU cc_start: 0.8058 (tp) cc_final: 0.7842 (tp) REVERT: D 159 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7788 (t0) outliers start: 37 outliers final: 21 residues processed: 135 average time/residue: 0.0889 time to fit residues: 16.5227 Evaluate side-chains 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.131334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.105009 restraints weight = 36092.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.108873 restraints weight = 19861.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.111472 restraints weight = 13139.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.113238 restraints weight = 9770.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.114338 restraints weight = 7899.832| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7913 Z= 0.140 Angle : 0.675 8.298 10788 Z= 0.349 Chirality : 0.043 0.147 1214 Planarity : 0.006 0.059 1373 Dihedral : 5.645 41.939 1087 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.37 % Favored : 91.43 % Rotamer: Outliers : 5.79 % Allowed : 23.72 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.11 % 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: -1.64 (0.27), residues: 1003 helix: -1.25 (0.72), residues: 43 sheet: -0.24 (0.29), residues: 352 loop : -1.66 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 54 TYR 0.020 0.002 TYR D 80 PHE 0.010 0.001 PHE E 163 TRP 0.022 0.002 TRP D 36 HIS 0.012 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7895) covalent geometry : angle 0.67341 (10752) SS BOND : bond 0.00313 ( 18) SS BOND : angle 0.99835 ( 36) hydrogen bonds : bond 0.03160 ( 197) hydrogen bonds : angle 7.14608 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8294 (p0) cc_final: 0.7916 (p0) REVERT: C 83 LEU cc_start: 0.8053 (mt) cc_final: 0.7751 (mt) REVERT: C 86 TYR cc_start: 0.8317 (m-80) cc_final: 0.8041 (m-80) REVERT: C 97 THR cc_start: 0.7650 (OUTLIER) cc_final: 0.7147 (p) REVERT: D 110 LEU cc_start: 0.8085 (tp) cc_final: 0.7863 (tp) REVERT: D 150 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7774 (mm-30) REVERT: D 159 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7814 (t0) REVERT: E 49 ILE cc_start: 0.7392 (mp) cc_final: 0.6990 (mm) outliers start: 51 outliers final: 35 residues processed: 133 average time/residue: 0.0831 time to fit residues: 15.4402 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.104504 restraints weight = 35845.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.108260 restraints weight = 19805.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.110899 restraints weight = 13122.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.112610 restraints weight = 9744.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.113632 restraints weight = 7864.366| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7913 Z= 0.134 Angle : 0.666 8.411 10788 Z= 0.345 Chirality : 0.043 0.166 1214 Planarity : 0.006 0.055 1373 Dihedral : 5.567 37.852 1087 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.08 % Favored : 91.72 % Rotamer: Outliers : 4.99 % Allowed : 25.09 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.11 % 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: -1.61 (0.27), residues: 1003 helix: -1.17 (0.74), residues: 42 sheet: -0.26 (0.29), residues: 349 loop : -1.61 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 142 TYR 0.026 0.002 TYR C 92 PHE 0.029 0.002 PHE B 29 TRP 0.044 0.002 TRP D 36 HIS 0.012 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7895) covalent geometry : angle 0.66536 (10752) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.91088 ( 36) hydrogen bonds : bond 0.03135 ( 197) hydrogen bonds : angle 6.96413 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8564 (p0) cc_final: 0.8205 (p0) REVERT: B 29 PHE cc_start: 0.6938 (t80) cc_final: 0.6720 (t80) REVERT: C 83 LEU cc_start: 0.8053 (mt) cc_final: 0.7801 (mt) REVERT: C 97 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7181 (p) REVERT: D 60 TYR cc_start: 0.7107 (m-80) cc_final: 0.6822 (m-80) REVERT: D 110 LEU cc_start: 0.8028 (tp) cc_final: 0.7822 (tp) REVERT: D 150 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: E 29 VAL cc_start: -0.0638 (OUTLIER) cc_final: -0.0894 (p) REVERT: E 47 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6814 (tp) outliers start: 44 outliers final: 33 residues processed: 126 average time/residue: 0.0866 time to fit residues: 15.1293 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.130187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.104349 restraints weight = 35824.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.108073 restraints weight = 20033.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.110527 restraints weight = 13307.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.112045 restraints weight = 9912.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.113392 restraints weight = 8108.478| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7913 Z= 0.127 Angle : 0.657 8.219 10788 Z= 0.338 Chirality : 0.043 0.147 1214 Planarity : 0.005 0.052 1373 Dihedral : 5.508 34.716 1087 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.87 % Favored : 90.83 % Rotamer: Outliers : 5.33 % Allowed : 24.74 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.61 (0.27), residues: 1003 helix: -1.18 (0.73), residues: 42 sheet: -0.35 (0.28), residues: 362 loop : -1.56 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 142 TYR 0.018 0.002 TYR D 193 PHE 0.018 0.002 PHE B 29 TRP 0.064 0.002 TRP D 36 HIS 0.011 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7895) covalent geometry : angle 0.65660 (10752) SS BOND : bond 0.00284 ( 18) SS BOND : angle 0.81669 ( 36) hydrogen bonds : bond 0.02918 ( 197) hydrogen bonds : angle 6.74959 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 96 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.8665 (p0) cc_final: 0.8354 (p0) REVERT: C 83 LEU cc_start: 0.7978 (mt) cc_final: 0.7643 (mt) REVERT: C 97 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7095 (p) REVERT: D 95 TYR cc_start: 0.6651 (m-80) cc_final: 0.5810 (m-80) REVERT: D 159 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7762 (t0) REVERT: E 29 VAL cc_start: -0.0385 (OUTLIER) cc_final: -0.0688 (p) REVERT: E 49 ILE cc_start: 0.7479 (mp) cc_final: 0.7006 (mm) outliers start: 47 outliers final: 32 residues processed: 128 average time/residue: 0.0882 time to fit residues: 15.7150 Evaluate side-chains 123 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.0770 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.103880 restraints weight = 35817.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.107555 restraints weight = 20140.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.110046 restraints weight = 13543.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.111537 restraints weight = 10115.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.112835 restraints weight = 8273.563| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7913 Z= 0.128 Angle : 0.648 8.234 10788 Z= 0.333 Chirality : 0.043 0.212 1214 Planarity : 0.006 0.064 1373 Dihedral : 5.399 27.892 1087 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.47 % Favored : 91.23 % Rotamer: Outliers : 4.65 % Allowed : 24.97 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.52 (0.27), residues: 1003 helix: -1.18 (0.72), residues: 42 sheet: -0.31 (0.28), residues: 361 loop : -1.48 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 142 TYR 0.017 0.002 TYR A 103 PHE 0.042 0.002 PHE B 29 TRP 0.072 0.003 TRP D 36 HIS 0.010 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7895) covalent geometry : angle 0.64787 (10752) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.78857 ( 36) hydrogen bonds : bond 0.02788 ( 197) hydrogen bonds : angle 6.62855 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8999 (mm) cc_final: 0.8780 (tp) REVERT: A 136 ASP cc_start: 0.8717 (p0) cc_final: 0.8439 (p0) REVERT: C 83 LEU cc_start: 0.8038 (mt) cc_final: 0.7735 (mt) REVERT: C 86 TYR cc_start: 0.8570 (m-80) cc_final: 0.8203 (m-10) REVERT: C 97 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7152 (p) REVERT: D 95 TYR cc_start: 0.6303 (m-80) cc_final: 0.6071 (m-80) REVERT: D 173 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6034 (pm20) REVERT: E 29 VAL cc_start: 0.0591 (OUTLIER) cc_final: 0.0296 (p) REVERT: E 49 ILE cc_start: 0.7305 (mp) cc_final: 0.7000 (mm) REVERT: E 192 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8995 (tp) outliers start: 41 outliers final: 33 residues processed: 127 average time/residue: 0.0867 time to fit residues: 15.1832 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.121704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.095647 restraints weight = 37391.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.098724 restraints weight = 22225.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.100756 restraints weight = 15379.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.102310 restraints weight = 11900.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.103093 restraints weight = 9872.243| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 7913 Z= 0.216 Angle : 0.750 9.219 10788 Z= 0.387 Chirality : 0.045 0.203 1214 Planarity : 0.006 0.060 1373 Dihedral : 5.954 26.527 1087 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.87 % Favored : 89.73 % Rotamer: Outliers : 5.68 % Allowed : 24.18 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.72 (0.27), residues: 1003 helix: -1.42 (0.65), residues: 42 sheet: -0.38 (0.28), residues: 343 loop : -1.64 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 142 TYR 0.030 0.003 TYR E 88 PHE 0.019 0.003 PHE B 29 TRP 0.048 0.003 TRP D 36 HIS 0.012 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7895) covalent geometry : angle 0.74727 (10752) SS BOND : bond 0.00558 ( 18) SS BOND : angle 1.26084 ( 36) hydrogen bonds : bond 0.03509 ( 197) hydrogen bonds : angle 7.15150 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8931 (tp) REVERT: C 105 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7107 (tm-30) REVERT: D 159 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7877 (t0) REVERT: E 99 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7793 (m-10) outliers start: 50 outliers final: 38 residues processed: 124 average time/residue: 0.0804 time to fit residues: 13.7089 Evaluate side-chains 122 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 0.0370 chunk 63 optimal weight: 0.3980 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.125403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.099042 restraints weight = 36340.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.102470 restraints weight = 20490.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.104933 restraints weight = 13799.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.106545 restraints weight = 10387.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.107345 restraints weight = 8464.794| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7913 Z= 0.151 Angle : 0.693 8.275 10788 Z= 0.357 Chirality : 0.044 0.173 1214 Planarity : 0.006 0.055 1373 Dihedral : 5.746 25.465 1087 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.47 % Favored : 90.13 % Rotamer: Outliers : 4.88 % Allowed : 24.86 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.72 (0.27), residues: 1003 helix: -1.31 (0.68), residues: 42 sheet: -0.41 (0.28), residues: 337 loop : -1.61 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 142 TYR 0.025 0.002 TYR D 33 PHE 0.011 0.002 PHE E 163 TRP 0.048 0.003 TRP D 36 HIS 0.014 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7895) covalent geometry : angle 0.69165 (10752) SS BOND : bond 0.00379 ( 18) SS BOND : angle 0.98675 ( 36) hydrogen bonds : bond 0.03120 ( 197) hydrogen bonds : angle 6.88171 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9126 (mm) cc_final: 0.8908 (tp) REVERT: C 83 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7685 (mt) REVERT: D 123 PHE cc_start: 0.7864 (m-80) cc_final: 0.7639 (m-80) outliers start: 43 outliers final: 39 residues processed: 121 average time/residue: 0.0823 time to fit residues: 13.7451 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 HIS ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.100215 restraints weight = 36140.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.103676 restraints weight = 20374.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.106143 restraints weight = 13677.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.107647 restraints weight = 10269.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.108451 restraints weight = 8435.361| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7913 Z= 0.133 Angle : 0.679 8.245 10788 Z= 0.348 Chirality : 0.043 0.148 1214 Planarity : 0.006 0.062 1373 Dihedral : 5.622 24.892 1087 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.17 % Favored : 90.43 % Rotamer: Outliers : 4.54 % Allowed : 25.43 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.67 (0.27), residues: 1003 helix: -1.27 (0.68), residues: 42 sheet: -0.39 (0.28), residues: 336 loop : -1.56 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 142 TYR 0.019 0.002 TYR D 180 PHE 0.010 0.002 PHE E 163 TRP 0.047 0.003 TRP D 36 HIS 0.010 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7895) covalent geometry : angle 0.67880 (10752) SS BOND : bond 0.00289 ( 18) SS BOND : angle 0.83400 ( 36) hydrogen bonds : bond 0.02960 ( 197) hydrogen bonds : angle 6.66185 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9105 (mm) cc_final: 0.8891 (tp) REVERT: C 83 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7609 (mt) REVERT: E 18 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7628 (mmt90) REVERT: E 49 ILE cc_start: 0.6954 (mm) cc_final: 0.6716 (mm) outliers start: 40 outliers final: 37 residues processed: 115 average time/residue: 0.0824 time to fit residues: 12.9756 Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 48 TRP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 chunk 78 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.126744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.100530 restraints weight = 36199.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.104128 restraints weight = 20383.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.106461 restraints weight = 13679.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.108194 restraints weight = 10256.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.109026 restraints weight = 8291.019| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7913 Z= 0.133 Angle : 0.672 8.344 10788 Z= 0.346 Chirality : 0.043 0.145 1214 Planarity : 0.006 0.059 1373 Dihedral : 5.563 25.904 1087 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.17 % Favored : 90.43 % Rotamer: Outliers : 4.43 % Allowed : 25.54 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.64 (0.27), residues: 1003 helix: -1.11 (0.70), residues: 42 sheet: -0.48 (0.28), residues: 342 loop : -1.48 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 142 TYR 0.020 0.002 TYR D 33 PHE 0.034 0.002 PHE C 10 TRP 0.045 0.003 TRP D 36 HIS 0.013 0.002 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7895) covalent geometry : angle 0.67173 (10752) SS BOND : bond 0.00319 ( 18) SS BOND : angle 0.82720 ( 36) hydrogen bonds : bond 0.02879 ( 197) hydrogen bonds : angle 6.53805 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.16 seconds wall clock time: 42 minutes 31.65 seconds (2551.65 seconds total)