Starting phenix.real_space_refine on Wed Feb 4 08:43:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dok_47085/02_2026/9dok_47085.map" } resolution = 3.26 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= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 37 5.16 5 C 6135 2.51 5 N 1632 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9510 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1849 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2763 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain: "F" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2866 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain: "G" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 5 Chain: "F" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.23, per 1000 atoms: 0.23 Number of scatterers: 9510 At special positions: 0 Unit cell: (71.28, 97.2, 143.64, 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 37 16.00 P 4 15.00 O 1702 8.00 N 1632 7.00 C 6135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 362.3 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 57.3% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.086A pdb=" N ILE B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.561A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.923A pdb=" N LEU B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 removed outlier: 3.989A pdb=" N SER B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.093A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.992A pdb=" N ILE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.999A pdb=" N LEU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.887A pdb=" N SER A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 4.073A pdb=" N ASP A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 2 through 36 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 55 through 63 removed outlier: 4.005A pdb=" N ARG G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 82 removed outlier: 3.587A pdb=" N LEU G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 removed outlier: 3.845A pdb=" N ILE G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 120 removed outlier: 3.513A pdb=" N ILE G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) Proline residue: G 105 - end of helix removed outlier: 3.852A pdb=" N VAL G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 136 Processing helix chain 'G' and resid 230 through 238 removed outlier: 3.569A pdb=" N THR G 236 " --> pdb=" O GLN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 removed outlier: 3.899A pdb=" N LEU G 244 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 260 Processing helix chain 'G' and resid 263 through 275 removed outlier: 3.617A pdb=" N LEU G 268 " --> pdb=" O ASN G 264 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA G 269 " --> pdb=" O ARG G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 293 Processing helix chain 'G' and resid 299 through 328 Proline residue: G 323 - end of helix removed outlier: 3.696A pdb=" N LEU G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 353 removed outlier: 3.531A pdb=" N ILE G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Proline residue: G 339 - end of helix Processing helix chain 'F' and resid 2 through 41 removed outlier: 3.541A pdb=" N ARG F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 95 through 120 removed outlier: 3.962A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Proline residue: F 105 - end of helix removed outlier: 3.559A pdb=" N LEU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 139 through 144 removed outlier: 4.034A pdb=" N LEU F 144 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.539A pdb=" N SER F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 247 " --> pdb=" O GLU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 3.857A pdb=" N PHE F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 256 through 261' Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'F' and resid 276 through 292 removed outlier: 3.790A pdb=" N VAL F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) Proline residue: F 290 - end of helix Processing helix chain 'F' and resid 304 through 327 Processing helix chain 'F' and resid 336 through 352 Processing helix chain 'F' and resid 352 through 365 Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 27 removed outlier: 6.659A pdb=" N ARG B 20 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 10 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL B 22 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS B 8 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU B 9 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.523A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 207 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 218 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 26 removed outlier: 6.719A pdb=" N ARG A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 10 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL A 22 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 8 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A 9 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.549A pdb=" N THR A 193 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 32 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 207 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 148 through 151 removed outlier: 3.990A pdb=" N VAL G 167 " --> pdb=" O GLN G 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 148 through 151 removed outlier: 6.198A pdb=" N TYR G 169 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG G 190 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE G 187 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL G 203 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 207 " --> pdb=" O GLU G 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 193 through 194 Processing sheet with id=AA8, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.273A pdb=" N ILE F 176 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 200 removed outlier: 3.951A pdb=" N THR F 199 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE F 211 " --> pdb=" O THR F 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 208 " --> pdb=" O LEU F 239 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1536 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: 1.12 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1730 1.33 - 1.45: 2266 1.45 - 1.57: 5609 1.57 - 1.69: 8 1.69 - 1.81: 68 Bond restraints: 9681 Sorted by residual: bond pdb=" C21 3PE G 402 " pdb=" O21 3PE G 402 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C31 3PE G 402 " pdb=" O31 3PE G 402 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" O13 3PE G 402 " pdb=" P 3PE G 402 " ideal model delta sigma weight residual 1.654 1.609 0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" O11 3PE G 402 " pdb=" P 3PE G 402 " ideal model delta sigma weight residual 1.644 1.610 0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" CA ALA G 135 " pdb=" C ALA G 135 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.82e+00 ... (remaining 9676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 12878 1.91 - 3.81: 151 3.81 - 5.72: 32 5.72 - 7.63: 4 7.63 - 9.54: 4 Bond angle restraints: 13069 Sorted by residual: angle pdb=" N ILE G 157 " pdb=" CA ILE G 157 " pdb=" C ILE G 157 " ideal model delta sigma weight residual 108.17 114.84 -6.67 1.40e+00 5.10e-01 2.27e+01 angle pdb=" N SER F 276 " pdb=" CA SER F 276 " pdb=" C SER F 276 " ideal model delta sigma weight residual 114.62 110.22 4.40 1.14e+00 7.69e-01 1.49e+01 angle pdb=" N ALA G 128 " pdb=" CA ALA G 128 " pdb=" C ALA G 128 " ideal model delta sigma weight residual 111.07 114.70 -3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" C2 3PE G 402 " pdb=" O21 3PE G 402 " pdb=" C21 3PE G 402 " ideal model delta sigma weight residual 121.04 111.50 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CA SER F 276 " pdb=" C SER F 276 " pdb=" N THR F 277 " ideal model delta sigma weight residual 119.71 116.01 3.70 1.17e+00 7.31e-01 9.98e+00 ... (remaining 13064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 5378 24.65 - 49.30: 423 49.30 - 73.96: 51 73.96 - 98.61: 14 98.61 - 123.26: 1 Dihedral angle restraints: 5867 sinusoidal: 2447 harmonic: 3420 Sorted by residual: dihedral pdb=" O21 3PE F 402 " pdb=" C2 3PE F 402 " pdb=" C3 3PE F 402 " pdb=" O31 3PE F 402 " ideal model delta sinusoidal sigma weight residual 60.47 -176.27 -123.26 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" CA ARG F 300 " pdb=" C ARG F 300 " pdb=" N PHE F 301 " pdb=" CA PHE F 301 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU G 202 " pdb=" CG GLU G 202 " pdb=" CD GLU G 202 " pdb=" OE1 GLU G 202 " ideal model delta sinusoidal sigma weight residual 0.00 -89.35 89.35 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1220 0.051 - 0.101: 231 0.101 - 0.152: 38 0.152 - 0.202: 1 0.202 - 0.253: 2 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CB ILE A 62 " pdb=" CA ILE A 62 " pdb=" CG1 ILE A 62 " pdb=" CG2 ILE A 62 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE F 32 " pdb=" CA ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CG2 ILE F 32 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1489 not shown) Planarity restraints: 1649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 152 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLN G 152 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN G 152 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY G 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 56 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO F 57 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 121 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO F 122 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 122 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 122 " 0.028 5.00e-02 4.00e+02 ... (remaining 1646 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 894 2.74 - 3.28: 9029 3.28 - 3.82: 15111 3.82 - 4.36: 17942 4.36 - 4.90: 32043 Nonbonded interactions: 75019 Sorted by model distance: nonbonded pdb=" OG1 THR G 195 " pdb=" N ASP G 196 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG F 251 " pdb=" OD2 ASP F 326 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR G 195 " pdb=" OD1 ASP G 196 " model vdw 2.281 3.040 nonbonded pdb=" NZ LYS B 177 " pdb=" OD2 ASP B 202 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG G 180 " pdb=" O ALA F 172 " model vdw 2.292 3.120 ... (remaining 75014 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 2 through 240) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.137 9681 Z= 0.175 Angle : 0.567 9.537 13069 Z= 0.295 Chirality : 0.041 0.253 1492 Planarity : 0.004 0.053 1649 Dihedral : 17.274 123.261 3677 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1190 helix: 1.41 (0.22), residues: 635 sheet: -1.18 (0.44), residues: 147 loop : -1.66 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.012 0.001 TYR F 209 PHE 0.012 0.001 PHE G 330 TRP 0.012 0.001 TRP G 250 HIS 0.004 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9681) covalent geometry : angle 0.56716 (13069) hydrogen bonds : bond 0.14567 ( 524) hydrogen bonds : angle 5.65514 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.364 Fit side-chains REVERT: F 152 MET cc_start: 0.7677 (ppp) cc_final: 0.7436 (ppp) REVERT: F 238 MET cc_start: 0.4274 (mmp) cc_final: 0.3338 (mmt) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1136 time to fit residues: 16.1914 Evaluate side-chains 103 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN G 197 HIS F 123 GLN F 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.144285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109029 restraints weight = 10706.062| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.30 r_work: 0.2831 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9681 Z= 0.253 Angle : 0.590 8.163 13069 Z= 0.306 Chirality : 0.045 0.235 1492 Planarity : 0.005 0.058 1649 Dihedral : 10.466 120.516 1490 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.74 % Allowed : 18.24 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1190 helix: 1.10 (0.21), residues: 637 sheet: -1.12 (0.44), residues: 143 loop : -1.65 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.014 0.001 TYR F 209 PHE 0.017 0.002 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9681) covalent geometry : angle 0.59033 (13069) hydrogen bonds : bond 0.05855 ( 524) hydrogen bonds : angle 4.59158 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.404 Fit side-chains REVERT: G 106 MET cc_start: 0.8669 (mmp) cc_final: 0.8464 (mmp) REVERT: G 177 ASP cc_start: 0.5134 (OUTLIER) cc_final: 0.4847 (m-30) REVERT: G 259 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6128 (mp10) REVERT: F 10 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7831 (mm-30) REVERT: F 152 MET cc_start: 0.7691 (ppp) cc_final: 0.7346 (ppp) REVERT: F 364 ARG cc_start: 0.7670 (mmt180) cc_final: 0.7315 (mmt-90) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 0.1066 time to fit residues: 19.1840 Evaluate side-chains 122 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 104 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.145878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.099273 restraints weight = 10675.418| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.53 r_work: 0.2823 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9681 Z= 0.131 Angle : 0.494 6.310 13069 Z= 0.260 Chirality : 0.041 0.213 1492 Planarity : 0.004 0.052 1649 Dihedral : 9.940 116.989 1490 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.23 % Allowed : 18.44 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1190 helix: 1.40 (0.21), residues: 637 sheet: -0.86 (0.46), residues: 137 loop : -1.57 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 180 TYR 0.014 0.001 TYR F 209 PHE 0.013 0.001 PHE G 330 TRP 0.011 0.001 TRP F 338 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9681) covalent geometry : angle 0.49362 (13069) hydrogen bonds : bond 0.04708 ( 524) hydrogen bonds : angle 4.32237 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8216 (mm-30) REVERT: G 106 MET cc_start: 0.8603 (mmp) cc_final: 0.8317 (mmp) REVERT: G 177 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4788 (m-30) REVERT: G 259 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: F 30 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8279 (mmp80) REVERT: F 238 MET cc_start: 0.4648 (mmp) cc_final: 0.4432 (mmp) REVERT: F 280 LEU cc_start: 0.8742 (mp) cc_final: 0.8500 (mp) REVERT: F 364 ARG cc_start: 0.7588 (mmt180) cc_final: 0.7274 (mmt-90) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 0.1115 time to fit residues: 18.6918 Evaluate side-chains 120 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 80 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS G 197 HIS F 150 GLN ** F 224 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.148074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105346 restraints weight = 10696.828| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.55 r_work: 0.2858 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9681 Z= 0.113 Angle : 0.471 6.261 13069 Z= 0.247 Chirality : 0.040 0.185 1492 Planarity : 0.004 0.050 1649 Dihedral : 9.331 110.965 1490 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.04 % Allowed : 18.44 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1190 helix: 1.63 (0.21), residues: 638 sheet: -0.72 (0.46), residues: 137 loop : -1.50 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 78 TYR 0.010 0.001 TYR F 209 PHE 0.013 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9681) covalent geometry : angle 0.47103 (13069) hydrogen bonds : bond 0.04189 ( 524) hydrogen bonds : angle 4.11730 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8986 (tpt) cc_final: 0.8669 (tpt) REVERT: A 119 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8259 (mm-30) REVERT: G 106 MET cc_start: 0.8569 (mmp) cc_final: 0.8304 (mmp) REVERT: G 259 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: F 280 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8543 (mp) REVERT: F 364 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7154 (mmt-90) outliers start: 30 outliers final: 15 residues processed: 130 average time/residue: 0.0960 time to fit residues: 17.7173 Evaluate side-chains 117 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.146713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.102546 restraints weight = 10698.495| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.79 r_work: 0.2820 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9681 Z= 0.135 Angle : 0.491 6.101 13069 Z= 0.254 Chirality : 0.041 0.238 1492 Planarity : 0.004 0.050 1649 Dihedral : 9.168 108.222 1490 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.43 % Allowed : 19.76 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1190 helix: 1.62 (0.21), residues: 638 sheet: -0.70 (0.45), residues: 137 loop : -1.45 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 157 TYR 0.023 0.001 TYR F 209 PHE 0.014 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.006 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9681) covalent geometry : angle 0.49116 (13069) hydrogen bonds : bond 0.04382 ( 524) hydrogen bonds : angle 4.12058 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7537 (mmtm) REVERT: G 106 MET cc_start: 0.8572 (mmp) cc_final: 0.8324 (mmp) REVERT: G 177 ASP cc_start: 0.5206 (OUTLIER) cc_final: 0.4959 (m-30) REVERT: G 259 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6821 (mp10) REVERT: F 238 MET cc_start: 0.4851 (mmp) cc_final: 0.3903 (mmt) REVERT: F 280 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8491 (mp) outliers start: 24 outliers final: 18 residues processed: 120 average time/residue: 0.0820 time to fit residues: 13.8394 Evaluate side-chains 121 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108617 restraints weight = 10641.426| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.38 r_work: 0.2843 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9681 Z= 0.145 Angle : 0.503 5.918 13069 Z= 0.259 Chirality : 0.041 0.221 1492 Planarity : 0.004 0.050 1649 Dihedral : 9.069 106.946 1490 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.14 % Allowed : 19.66 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1190 helix: 1.60 (0.21), residues: 638 sheet: -0.69 (0.45), residues: 137 loop : -1.42 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.017 0.001 TYR F 209 PHE 0.014 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.004 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9681) covalent geometry : angle 0.50279 (13069) hydrogen bonds : bond 0.04478 ( 524) hydrogen bonds : angle 4.11903 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8990 (tpt) cc_final: 0.8697 (tpt) REVERT: A 115 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7530 (mmtm) REVERT: G 106 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8343 (mmp) REVERT: G 177 ASP cc_start: 0.5298 (OUTLIER) cc_final: 0.5030 (m-30) REVERT: G 259 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: F 238 MET cc_start: 0.5163 (mmp) cc_final: 0.4446 (mmt) REVERT: F 280 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8514 (mp) outliers start: 31 outliers final: 21 residues processed: 125 average time/residue: 0.0858 time to fit residues: 15.0959 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** 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 = 0.3551 r_free = 0.3551 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099321 restraints weight = 10798.093| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.58 r_work: 0.2794 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9681 Z= 0.216 Angle : 0.551 6.241 13069 Z= 0.284 Chirality : 0.044 0.232 1492 Planarity : 0.004 0.050 1649 Dihedral : 9.248 106.756 1490 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.24 % Allowed : 19.25 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1190 helix: 1.38 (0.21), residues: 637 sheet: -0.77 (0.44), residues: 137 loop : -1.46 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.016 0.001 TYR F 209 PHE 0.017 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9681) covalent geometry : angle 0.55060 (13069) hydrogen bonds : bond 0.05125 ( 524) hydrogen bonds : angle 4.24468 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8991 (tpt) cc_final: 0.8773 (tpt) REVERT: A 115 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7557 (mmtm) REVERT: G 177 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.5088 (m-30) REVERT: G 259 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: F 238 MET cc_start: 0.5111 (mmp) cc_final: 0.4313 (mmt) REVERT: F 280 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8457 (mp) outliers start: 32 outliers final: 24 residues processed: 128 average time/residue: 0.0975 time to fit residues: 17.5365 Evaluate side-chains 131 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 90 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** 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 = 0.3564 r_free = 0.3564 target = 0.144767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.099989 restraints weight = 10716.648| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.72 r_work: 0.2814 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9681 Z= 0.129 Angle : 0.500 5.764 13069 Z= 0.259 Chirality : 0.041 0.192 1492 Planarity : 0.004 0.049 1649 Dihedral : 9.013 105.785 1490 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.14 % Allowed : 19.76 % Favored : 77.10 % 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: 0.39 (0.25), residues: 1190 helix: 1.57 (0.21), residues: 637 sheet: -0.72 (0.44), residues: 143 loop : -1.48 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 265 TYR 0.017 0.001 TYR F 209 PHE 0.014 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.004 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9681) covalent geometry : angle 0.50002 (13069) hydrogen bonds : bond 0.04450 ( 524) hydrogen bonds : angle 4.11354 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7443 (mmtm) REVERT: G 177 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.5081 (m-30) REVERT: G 259 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: F 238 MET cc_start: 0.5248 (mmp) cc_final: 0.4914 (mmp) REVERT: F 280 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8426 (mp) outliers start: 31 outliers final: 24 residues processed: 124 average time/residue: 0.0964 time to fit residues: 16.9965 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.0040 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.101667 restraints weight = 10599.758| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.57 r_work: 0.2846 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9681 Z= 0.133 Angle : 0.500 5.745 13069 Z= 0.258 Chirality : 0.041 0.242 1492 Planarity : 0.004 0.048 1649 Dihedral : 8.884 104.900 1490 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.24 % Allowed : 19.86 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1190 helix: 1.60 (0.21), residues: 637 sheet: -0.81 (0.43), residues: 149 loop : -1.43 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.016 0.001 TYR F 209 PHE 0.014 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.004 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9681) covalent geometry : angle 0.50010 (13069) hydrogen bonds : bond 0.04392 ( 524) hydrogen bonds : angle 4.08358 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.8951 (tpt) cc_final: 0.8637 (tpt) REVERT: A 115 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7469 (mmtm) REVERT: G 177 ASP cc_start: 0.5186 (OUTLIER) cc_final: 0.4946 (m-30) REVERT: G 259 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: F 238 MET cc_start: 0.5566 (mmp) cc_final: 0.5210 (mmp) REVERT: F 280 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8486 (mp) outliers start: 32 outliers final: 27 residues processed: 126 average time/residue: 0.1056 time to fit residues: 18.7847 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 197 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 197 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105231 restraints weight = 10695.866| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.68 r_work: 0.2770 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9681 Z= 0.197 Angle : 0.549 8.828 13069 Z= 0.283 Chirality : 0.043 0.266 1492 Planarity : 0.004 0.049 1649 Dihedral : 9.004 104.594 1490 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.94 % Allowed : 19.96 % Favored : 77.10 % 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: 0.24 (0.25), residues: 1190 helix: 1.44 (0.21), residues: 637 sheet: -0.87 (0.43), residues: 149 loop : -1.49 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.015 0.001 TYR F 209 PHE 0.016 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.006 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9681) covalent geometry : angle 0.54925 (13069) hydrogen bonds : bond 0.04915 ( 524) hydrogen bonds : angle 4.16601 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7623 (mmtm) REVERT: G 177 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4939 (m-30) REVERT: G 255 TYR cc_start: 0.8535 (t80) cc_final: 0.8261 (t80) REVERT: G 259 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: F 162 GLU cc_start: 0.6337 (tm-30) cc_final: 0.6128 (tm-30) REVERT: F 238 MET cc_start: 0.5600 (mmp) cc_final: 0.5240 (mmp) REVERT: F 280 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8461 (mp) outliers start: 29 outliers final: 24 residues processed: 126 average time/residue: 0.1007 time to fit residues: 17.9421 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 240 GLU Chi-restraints excluded: chain G residue 251 GLN Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 150 GLN Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS F 150 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098224 restraints weight = 10638.125| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.50 r_work: 0.2835 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9681 Z= 0.121 Angle : 0.501 8.614 13069 Z= 0.259 Chirality : 0.041 0.239 1492 Planarity : 0.004 0.048 1649 Dihedral : 8.824 103.936 1490 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.43 % Allowed : 20.67 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1190 helix: 1.64 (0.21), residues: 637 sheet: -0.78 (0.44), residues: 143 loop : -1.42 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.016 0.001 TYR F 209 PHE 0.020 0.001 PHE F 149 TRP 0.011 0.001 TRP F 338 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9681) covalent geometry : angle 0.50115 (13069) hydrogen bonds : bond 0.04301 ( 524) hydrogen bonds : angle 4.03299 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.54 seconds wall clock time: 42 minutes 54.30 seconds (2574.30 seconds total)