Starting phenix.real_space_refine on Thu Jul 2 18:43:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/07_2026/8yjh_39342.cif" } resolution = 3.68 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 63 5.16 5 C 5965 2.51 5 N 1631 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9735 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9735 At special positions: 0 Unit cell: (106.24, 95.45, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 53 15.00 O 2023 8.00 N 1631 7.00 C 5965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " 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: 0.95 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 28.9% alpha, 25.4% beta 14 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.262A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.975A pdb=" N LEU B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 222 " --> pdb=" O THR B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.729A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 209 through 217 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.528A pdb=" N LEU C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 222 " --> pdb=" O THR C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'A' and resid 8 through 19 removed outlier: 4.365A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.744A pdb=" N ALA D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.711A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.561A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.767A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.967A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 252 removed outlier: 3.650A pdb=" N VAL D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.744A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.503A pdb=" N PHE D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.836A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.713A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 47 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 238 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.563A pdb=" N VAL B 111 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 207 removed outlier: 4.523A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 167 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 88 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.863A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 251 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 238 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 136 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 198 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 127 removed outlier: 3.753A pdb=" N GLY D 348 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C 127 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 346 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 208 removed outlier: 4.863A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 3.620A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 249 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 136 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 198 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.571A pdb=" N ARG D 19 " --> pdb=" O GLU D 206 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 204 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.799A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2732 1.34 - 1.46: 2131 1.46 - 1.58: 4920 1.58 - 1.70: 102 1.70 - 1.82: 102 Bond restraints: 9987 Sorted by residual: bond pdb=" C3' DT J 8 " pdb=" C2' DT J 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT E 5 " pdb=" C2' DT E 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 bond pdb=" C THR C 219 " pdb=" N PRO C 220 " ideal model delta sigma weight residual 1.335 1.362 -0.027 9.40e-03 1.13e+04 8.22e+00 bond pdb=" C1' DT E 25 " pdb=" N1 DT E 25 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.04e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13066 2.27 - 4.53: 505 4.53 - 6.80: 78 6.80 - 9.06: 37 9.06 - 11.33: 10 Bond angle restraints: 13696 Sorted by residual: angle pdb=" CA GLU B 132 " pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.16e+01 angle pdb=" O GLN A 131 " pdb=" C GLN A 131 " pdb=" N GLU A 132 " ideal model delta sigma weight residual 122.39 128.16 -5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" C LYS B 254 " pdb=" N ILE B 255 " pdb=" CA ILE B 255 " ideal model delta sigma weight residual 121.70 129.65 -7.95 1.80e+00 3.09e-01 1.95e+01 angle pdb=" N3 DT H 3 " pdb=" C4 DT H 3 " pdb=" O4 DT H 3 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 13691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5024 17.60 - 35.19: 688 35.19 - 52.79: 280 52.79 - 70.38: 48 70.38 - 87.98: 13 Dihedral angle restraints: 6053 sinusoidal: 2807 harmonic: 3246 Sorted by residual: dihedral pdb=" CA MET C 199 " pdb=" C MET C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASN B 71 " pdb=" C ASN B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE D 33 " pdb=" C ILE D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.56 22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1132 0.054 - 0.108: 339 0.108 - 0.162: 80 0.162 - 0.216: 21 0.216 - 0.270: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL A 236 " pdb=" CA VAL A 236 " pdb=" CG1 VAL A 236 " pdb=" CG2 VAL A 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1575 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 274 " -0.020 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP D 274 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP D 274 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 274 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 274 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 274 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 132 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C GLU A 132 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 132 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 133 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.236 9.50e-02 1.11e+02 1.07e-01 8.83e+00 pdb=" NE ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1834 2.79 - 3.31: 8023 3.31 - 3.84: 17211 3.84 - 4.37: 19369 4.37 - 4.90: 32874 Nonbonded interactions: 79311 Sorted by model distance: nonbonded pdb=" OE2 GLU A 192 " pdb=" OG SER A 223 " model vdw 2.256 3.040 nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.306 3.040 nonbonded pdb=" O THR C 216 " pdb=" OG1 THR C 219 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR C 211 " pdb=" O SER D 25 " model vdw 2.357 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.366 3.040 ... (remaining 79306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 254) selection = (chain 'C' and resid 1 through 254) } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.100 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.006 0.062 9988 Z= 0.339 Angle : 1.073 11.331 13698 Z= 0.635 Chirality : 0.058 0.270 1578 Planarity : 0.007 0.107 1583 Dihedral : 18.972 87.975 3944 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.21), residues: 1107 helix: -2.74 (0.20), residues: 307 sheet: -2.02 (0.27), residues: 331 loop : -2.36 (0.23), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 5 TYR 0.022 0.003 TYR B 133 PHE 0.037 0.003 PHE D 27 TRP 0.062 0.004 TRP D 274 HIS 0.007 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.34 ( 9987) covalent geometry : angle 1.07281 / 0.64 (13696) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 2.40126 / 1.33 ( 2) hydrogen bonds : bond 0.19943 / 13.08 ( 431) hydrogen bonds : angle 9.94013 / 6.93 ( 1208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.316 Fit side-chains REVERT: B 184 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 201 GLU cc_start: 0.7192 (pt0) cc_final: 0.6920 (pt0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0701 time to fit residues: 17.5058 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 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 = 0.3949 r_free = 0.3949 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113103 restraints weight = 14656.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115810 restraints weight = 9776.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117700 restraints weight = 7333.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118851 restraints weight = 5983.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119925 restraints weight = 5212.940| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9988 Z= 0.188 Angle : 0.661 6.245 13698 Z= 0.356 Chirality : 0.047 0.228 1578 Planarity : 0.005 0.043 1583 Dihedral : 19.316 78.654 1802 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.93 % Allowed : 7.95 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.22), residues: 1107 helix: -0.93 (0.27), residues: 304 sheet: -1.94 (0.26), residues: 327 loop : -2.06 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 5 TYR 0.013 0.002 TYR C 211 PHE 0.013 0.001 PHE D 126 TRP 0.029 0.002 TRP D 274 HIS 0.005 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 9987) covalent geometry : angle 0.66065 / 0.36 (13696) SS BOND : bond 0.00319 / 0.17 ( 1) SS BOND : angle 0.37197 / 0.21 ( 2) hydrogen bonds : bond 0.04710 / 2.99 ( 431) hydrogen bonds : angle 7.10802 / 4.94 ( 1208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.366 Fit side-chains REVERT: B 86 ASP cc_start: 0.7700 (m-30) cc_final: 0.7456 (t0) REVERT: B 177 ASN cc_start: 0.7741 (t0) cc_final: 0.7417 (t0) REVERT: B 199 MET cc_start: 0.7537 (tmm) cc_final: 0.6975 (tpp) REVERT: C 201 GLU cc_start: 0.7248 (pt0) cc_final: 0.6991 (pt0) REVERT: D 127 THR cc_start: 0.8850 (p) cc_final: 0.8534 (t) outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 0.0580 time to fit residues: 13.2870 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.0470 chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.0050 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.3230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 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 = 0.3963 r_free = 0.3963 target = 0.145423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114436 restraints weight = 14628.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117230 restraints weight = 9645.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119218 restraints weight = 7185.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120577 restraints weight = 5828.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121525 restraints weight = 5009.195| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9988 Z= 0.121 Angle : 0.571 7.134 13698 Z= 0.311 Chirality : 0.044 0.222 1578 Planarity : 0.004 0.038 1583 Dihedral : 19.295 73.945 1802 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.14 % Allowed : 11.76 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1107 helix: -0.26 (0.29), residues: 306 sheet: -1.84 (0.26), residues: 327 loop : -1.84 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.012 0.001 TYR A 250 PHE 0.009 0.001 PHE D 126 TRP 0.043 0.002 TRP D 274 HIS 0.005 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 9987) covalent geometry : angle 0.57110 / 0.31 (13696) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 1.01056 / 0.55 ( 2) hydrogen bonds : bond 0.03869 / 2.50 ( 431) hydrogen bonds : angle 6.60876 / 4.59 ( 1208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.332 Fit side-chains REVERT: B 177 ASN cc_start: 0.7782 (t0) cc_final: 0.7472 (t0) REVERT: B 199 MET cc_start: 0.7412 (tmm) cc_final: 0.7124 (tpp) REVERT: C 121 LEU cc_start: 0.8377 (tp) cc_final: 0.7934 (tt) REVERT: A 68 MET cc_start: 0.7921 (ptp) cc_final: 0.7634 (ptp) REVERT: A 135 CYS cc_start: 0.8112 (p) cc_final: 0.7837 (p) REVERT: D 40 TYR cc_start: 0.7743 (m-10) cc_final: 0.7352 (m-10) outliers start: 11 outliers final: 4 residues processed: 136 average time/residue: 0.0581 time to fit residues: 12.4476 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 90 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110571 restraints weight = 14687.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113322 restraints weight = 9818.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115250 restraints weight = 7386.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116613 restraints weight = 6024.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117594 restraints weight = 5218.539| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9988 Z= 0.167 Angle : 0.585 7.229 13698 Z= 0.313 Chirality : 0.045 0.194 1578 Planarity : 0.003 0.036 1583 Dihedral : 19.188 75.034 1802 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.14 % Allowed : 13.62 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.24), residues: 1107 helix: 0.23 (0.29), residues: 309 sheet: -1.85 (0.26), residues: 331 loop : -1.71 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.013 0.002 TYR A 250 PHE 0.016 0.002 PHE D 126 TRP 0.023 0.001 TRP D 274 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 9987) covalent geometry : angle 0.58487 / 0.31 (13696) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 0.65033 / 0.34 ( 2) hydrogen bonds : bond 0.03646 / 2.37 ( 431) hydrogen bonds : angle 6.17819 / 4.30 ( 1208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.355 Fit side-chains REVERT: B 177 ASN cc_start: 0.7779 (t0) cc_final: 0.7480 (t0) REVERT: C 121 LEU cc_start: 0.8444 (tp) cc_final: 0.8026 (tt) REVERT: A 68 MET cc_start: 0.7980 (ptp) cc_final: 0.7743 (ptp) REVERT: A 135 CYS cc_start: 0.8126 (p) cc_final: 0.7845 (p) REVERT: D 127 THR cc_start: 0.8921 (p) cc_final: 0.8626 (t) REVERT: D 274 TRP cc_start: 0.7467 (t60) cc_final: 0.7219 (t60) REVERT: D 326 LYS cc_start: 0.8088 (pttm) cc_final: 0.7346 (mmtp) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.0819 time to fit residues: 16.9635 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.141970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110428 restraints weight = 14622.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113206 restraints weight = 9691.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115156 restraints weight = 7249.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116444 restraints weight = 5906.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117452 restraints weight = 5135.396| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9988 Z= 0.151 Angle : 0.574 8.986 13698 Z= 0.306 Chirality : 0.044 0.201 1578 Planarity : 0.003 0.033 1583 Dihedral : 19.124 74.881 1802 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.86 % Allowed : 14.04 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1107 helix: 0.45 (0.29), residues: 308 sheet: -1.93 (0.26), residues: 311 loop : -1.57 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.015 0.002 TYR A 250 PHE 0.010 0.001 PHE D 126 TRP 0.018 0.001 TRP D 274 HIS 0.004 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9987) covalent geometry : angle 0.57378 / 0.31 (13696) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.74215 / 0.39 ( 2) hydrogen bonds : bond 0.03486 / 2.26 ( 431) hydrogen bonds : angle 6.04072 / 4.18 ( 1208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.447 Fit side-chains REVERT: B 199 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6465 (tpp) REVERT: A 68 MET cc_start: 0.7935 (ptp) cc_final: 0.7593 (ptp) REVERT: A 135 CYS cc_start: 0.8115 (p) cc_final: 0.7848 (p) REVERT: D 127 THR cc_start: 0.8966 (p) cc_final: 0.8652 (t) REVERT: D 274 TRP cc_start: 0.7430 (t60) cc_final: 0.7088 (t60) REVERT: D 326 LYS cc_start: 0.8132 (pttm) cc_final: 0.7378 (mmtp) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.0818 time to fit residues: 17.6089 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 67 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3874 r_free = 0.3874 target = 0.138482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107212 restraints weight = 14702.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110293 restraints weight = 10279.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111195 restraints weight = 7708.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111505 restraints weight = 6462.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111641 restraints weight = 6082.099| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9988 Z= 0.204 Angle : 0.624 9.937 13698 Z= 0.326 Chirality : 0.045 0.234 1578 Planarity : 0.003 0.032 1583 Dihedral : 19.060 74.146 1802 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 15.17 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.24), residues: 1107 helix: 0.48 (0.29), residues: 308 sheet: -1.96 (0.26), residues: 309 loop : -1.51 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 211 TYR 0.016 0.002 TYR B 133 PHE 0.020 0.002 PHE A 215 TRP 0.015 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 9987) covalent geometry : angle 0.62417 / 0.33 (13696) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.98256 / 0.52 ( 2) hydrogen bonds : bond 0.03733 / 2.47 ( 431) hydrogen bonds : angle 5.96324 / 4.13 ( 1208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.389 Fit side-chains REVERT: B 36 ASN cc_start: 0.8460 (m-40) cc_final: 0.8214 (m-40) REVERT: B 86 ASP cc_start: 0.7477 (m-30) cc_final: 0.7045 (t70) REVERT: B 177 ASN cc_start: 0.7840 (t0) cc_final: 0.7562 (t0) REVERT: C 75 MET cc_start: 0.8864 (ttt) cc_final: 0.8548 (ttt) REVERT: A 135 CYS cc_start: 0.8234 (p) cc_final: 0.7965 (p) REVERT: D 326 LYS cc_start: 0.8253 (pttm) cc_final: 0.7524 (mmtp) outliers start: 23 outliers final: 14 residues processed: 141 average time/residue: 0.0826 time to fit residues: 17.4455 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.7980 chunk 10 optimal weight: 0.0070 chunk 106 optimal weight: 0.4980 chunk 13 optimal weight: 0.0370 chunk 110 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3911 r_free = 0.3911 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110221 restraints weight = 14429.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112914 restraints weight = 9470.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114863 restraints weight = 7057.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116217 restraints weight = 5737.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117165 restraints weight = 4957.977| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9988 Z= 0.122 Angle : 0.582 9.608 13698 Z= 0.306 Chirality : 0.045 0.239 1578 Planarity : 0.003 0.033 1583 Dihedral : 18.953 75.064 1802 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.75 % Allowed : 16.92 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.24), residues: 1107 helix: 0.64 (0.29), residues: 309 sheet: -1.90 (0.26), residues: 311 loop : -1.43 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 129 TYR 0.017 0.002 TYR A 250 PHE 0.009 0.001 PHE D 126 TRP 0.042 0.002 TRP D 274 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9987) covalent geometry : angle 0.58229 / 0.31 (13696) SS BOND : bond 0.00052 / 0.03 ( 1) SS BOND : angle 0.64887 / 0.34 ( 2) hydrogen bonds : bond 0.03228 / 2.09 ( 431) hydrogen bonds : angle 5.80272 / 4.02 ( 1208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.230 Fit side-chains REVERT: B 86 ASP cc_start: 0.7216 (m-30) cc_final: 0.6993 (t70) REVERT: B 108 GLN cc_start: 0.7590 (mp10) cc_final: 0.7342 (mp10) REVERT: B 177 ASN cc_start: 0.7853 (t0) cc_final: 0.7590 (t0) REVERT: B 199 MET cc_start: 0.7218 (tpp) cc_final: 0.6182 (tpp) REVERT: C 244 MET cc_start: 0.8835 (ttm) cc_final: 0.8563 (ttm) REVERT: A 135 CYS cc_start: 0.8135 (p) cc_final: 0.7927 (p) REVERT: D 127 THR cc_start: 0.8836 (p) cc_final: 0.8540 (t) REVERT: D 326 LYS cc_start: 0.8219 (pttm) cc_final: 0.7537 (mmtp) outliers start: 17 outliers final: 12 residues processed: 141 average time/residue: 0.0679 time to fit residues: 14.5103 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 233 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3877 r_free = 0.3877 target = 0.138861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107438 restraints weight = 14546.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110792 restraints weight = 10801.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111296 restraints weight = 7567.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111561 restraints weight = 6808.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112226 restraints weight = 6194.003| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9988 Z= 0.185 Angle : 0.613 10.790 13698 Z= 0.318 Chirality : 0.045 0.221 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.912 75.064 1802 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 17.54 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1107 helix: 0.66 (0.29), residues: 309 sheet: -1.98 (0.26), residues: 311 loop : -1.31 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 339 TYR 0.014 0.002 TYR D 26 PHE 0.013 0.002 PHE D 126 TRP 0.030 0.002 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 9987) covalent geometry : angle 0.61244 / 0.32 (13696) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 1.22076 / 0.65 ( 2) hydrogen bonds : bond 0.03497 / 2.29 ( 431) hydrogen bonds : angle 5.75644 / 3.99 ( 1208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.243 Fit side-chains REVERT: B 86 ASP cc_start: 0.7357 (m-30) cc_final: 0.7134 (t70) REVERT: B 108 GLN cc_start: 0.7682 (mp10) cc_final: 0.7334 (mp10) REVERT: B 177 ASN cc_start: 0.7901 (t0) cc_final: 0.7626 (t0) REVERT: D 44 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8472 (mp) REVERT: D 127 THR cc_start: 0.8858 (p) cc_final: 0.8539 (t) REVERT: D 326 LYS cc_start: 0.8236 (pttm) cc_final: 0.7600 (mmtp) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.0732 time to fit residues: 14.4149 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 101 optimal weight: 0.0010 chunk 52 optimal weight: 0.7980 chunk 13 optimal weight: 0.0000 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3913 r_free = 0.3913 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110483 restraints weight = 14467.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113281 restraints weight = 9461.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115226 restraints weight = 7003.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116485 restraints weight = 5704.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117526 restraints weight = 4952.153| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9988 Z= 0.116 Angle : 0.568 10.125 13698 Z= 0.299 Chirality : 0.044 0.211 1578 Planarity : 0.003 0.033 1583 Dihedral : 18.815 75.267 1802 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.75 % Allowed : 17.75 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.25), residues: 1107 helix: 0.82 (0.29), residues: 308 sheet: -1.90 (0.26), residues: 313 loop : -1.24 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 5 TYR 0.013 0.001 TYR A 250 PHE 0.008 0.001 PHE C 169 TRP 0.022 0.002 TRP D 274 HIS 0.003 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9987) covalent geometry : angle 0.56795 / 0.30 (13696) SS BOND : bond 0.00039 / 0.02 ( 1) SS BOND : angle 0.71708 / 0.38 ( 2) hydrogen bonds : bond 0.03108 / 2.02 ( 431) hydrogen bonds : angle 5.62011 / 3.90 ( 1208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.355 Fit side-chains REVERT: B 108 GLN cc_start: 0.7650 (mp10) cc_final: 0.7414 (mp10) REVERT: B 177 ASN cc_start: 0.7889 (t0) cc_final: 0.7653 (t0) REVERT: C 91 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6198 (mtm110) REVERT: C 244 MET cc_start: 0.8691 (ttm) cc_final: 0.8475 (ttm) REVERT: D 44 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8498 (mp) REVERT: D 127 THR cc_start: 0.8960 (p) cc_final: 0.8658 (t) REVERT: D 326 LYS cc_start: 0.8322 (pttm) cc_final: 0.7623 (mmtp) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.0698 time to fit residues: 14.2260 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 0.0070 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3898 r_free = 0.3898 target = 0.140282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108985 restraints weight = 14443.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111682 restraints weight = 9515.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113615 restraints weight = 7109.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114848 restraints weight = 5797.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115816 restraints weight = 5057.890| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9988 Z= 0.148 Angle : 0.589 10.088 13698 Z= 0.306 Chirality : 0.044 0.193 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.768 75.218 1802 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 18.16 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1107 helix: 0.86 (0.29), residues: 308 sheet: -1.83 (0.27), residues: 311 loop : -1.21 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.013 0.002 TYR A 250 PHE 0.011 0.002 PHE D 126 TRP 0.020 0.001 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9987) covalent geometry : angle 0.58927 / 0.31 (13696) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 0.96952 / 0.51 ( 2) hydrogen bonds : bond 0.03262 / 2.14 ( 431) hydrogen bonds : angle 5.57553 / 3.87 ( 1208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.332 Fit side-chains REVERT: B 108 GLN cc_start: 0.7624 (mp10) cc_final: 0.7346 (mp10) REVERT: B 177 ASN cc_start: 0.7858 (t0) cc_final: 0.7624 (t0) REVERT: C 91 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6176 (mtm110) REVERT: D 44 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8520 (mp) REVERT: D 127 THR cc_start: 0.8946 (p) cc_final: 0.8641 (t) REVERT: D 326 LYS cc_start: 0.8344 (pttm) cc_final: 0.7645 (mmtp) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.0777 time to fit residues: 14.8585 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0000 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 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 = 0.3909 r_free = 0.3909 target = 0.141196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109731 restraints weight = 14335.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112449 restraints weight = 9499.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114416 restraints weight = 7059.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115771 restraints weight = 5724.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116615 restraints weight = 4965.624| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9988 Z= 0.135 Angle : 0.588 11.839 13698 Z= 0.304 Chirality : 0.044 0.208 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.720 74.374 1802 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.34 % Allowed : 18.78 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1107 helix: 0.87 (0.29), residues: 308 sheet: -1.81 (0.27), residues: 311 loop : -1.19 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.013 0.002 TYR A 250 PHE 0.009 0.001 PHE D 126 TRP 0.020 0.001 TRP D 274 HIS 0.004 0.001 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 9987) covalent geometry : angle 0.58780 / 0.30 (13696) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 0.83941 / 0.44 ( 2) hydrogen bonds : bond 0.03161 / 2.07 ( 431) hydrogen bonds : angle 5.52667 / 3.83 ( 1208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.03 seconds wall clock time: 26 minutes 48.00 seconds (1608.00 seconds total)