Starting phenix.real_space_refine on Tue Nov 18 04:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.map" model { file = "/net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gch_51230/11_2025/9gch_51230.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians P 70 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 6828 2.51 5 N 1971 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11231 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "F" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2355 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Chain: "T" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1415 Classifications: {'RNA': 67} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 23, 'rna3p_pyr': 27} Link IDs: {'rna2p': 16, 'rna3p': 50} Chain breaks: 1 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.99, per 1000 atoms: 0.27 Number of scatterers: 11231 At special positions: 0 Unit cell: (103.644, 97.3417, 135.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 70 15.00 Mg 1 11.99 O 2313 8.00 N 1971 7.00 C 6828 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 502.9 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 54.1% alpha, 11.9% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.560A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.790A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.547A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.526A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.804A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.501A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.807A pdb=" N GLY C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.558A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.629A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.510A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.520A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.853A pdb=" N GLY D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.456A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'F' and resid 93 through 104 removed outlier: 4.113A pdb=" N GLU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.945A pdb=" N GLU F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS F 123 " --> pdb=" O THR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 164 removed outlier: 3.502A pdb=" N ALA F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.556A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 237 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.711A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 329 removed outlier: 3.546A pdb=" N LEU F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.605A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.599A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.569A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.619A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.212A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 342 through 344 removed outlier: 4.474A pdb=" N GLY F 383 " --> pdb=" O GLN F 343 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.33 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: 3069 1.34 - 1.46: 3182 1.46 - 1.58: 5073 1.58 - 1.71: 137 1.71 - 1.83: 81 Bond restraints: 11542 Sorted by residual: bond pdb=" P U T 2 " pdb=" OP2 U T 2 " ideal model delta sigma weight residual 1.485 1.561 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" CG HIS F 242 " pdb=" CD2 HIS F 242 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.35e+00 bond pdb=" CE1 HIS F 242 " pdb=" NE2 HIS F 242 " ideal model delta sigma weight residual 1.321 1.294 0.027 1.00e-02 1.00e+04 7.19e+00 bond pdb=" C5' GTP T 101 " pdb=" O5' GTP T 101 " ideal model delta sigma weight residual 1.410 1.463 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" O5' U T 52 " pdb=" C5' U T 52 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.17e+00 ... (remaining 11537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 15568 2.21 - 4.42: 351 4.42 - 6.64: 18 6.64 - 8.85: 7 8.85 - 11.06: 4 Bond angle restraints: 15948 Sorted by residual: angle pdb=" OG1 THR C 110 " pdb=" CB THR C 110 " pdb=" CG2 THR C 110 " ideal model delta sigma weight residual 109.30 101.30 8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" C4' GTP T 101 " pdb=" C3' GTP T 101 " pdb=" O3' GTP T 101 " ideal model delta sigma weight residual 109.47 98.41 11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B GTP T 101 " pdb=" PB GTP T 101 " pdb=" O2B GTP T 101 " ideal model delta sigma weight residual 109.50 120.13 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C2' GTP T 101 " pdb=" C3' GTP T 101 " pdb=" O3' GTP T 101 " ideal model delta sigma weight residual 109.47 119.88 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" OG1 THR A 110 " pdb=" CB THR A 110 " pdb=" CG2 THR A 110 " ideal model delta sigma weight residual 109.30 102.69 6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 15943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 6783 35.70 - 71.39: 209 71.39 - 107.09: 38 107.09 - 142.78: 1 142.78 - 178.48: 3 Dihedral angle restraints: 7034 sinusoidal: 3374 harmonic: 3660 Sorted by residual: dihedral pdb=" O4' C T 44 " pdb=" C1' C T 44 " pdb=" N1 C T 44 " pdb=" C2 C T 44 " ideal model delta sinusoidal sigma weight residual 232.00 53.52 178.48 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C8 GTP T 101 " pdb=" C1' GTP T 101 " pdb=" N9 GTP T 101 " pdb=" O4' GTP T 101 " ideal model delta sinusoidal sigma weight residual 104.59 -63.20 167.79 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP T 101 " pdb=" O5' GTP T 101 " pdb=" PA GTP T 101 " pdb=" O3A GTP T 101 " ideal model delta sinusoidal sigma weight residual 69.27 -137.17 -153.56 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 7031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1678 0.104 - 0.207: 219 0.207 - 0.311: 2 0.311 - 0.415: 0 0.415 - 0.518: 2 Chirality restraints: 1901 Sorted by residual: chirality pdb=" P A T 19 " pdb=" OP1 A T 19 " pdb=" OP2 A T 19 " pdb=" O5' A T 19 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" P U T 2 " pdb=" OP1 U T 2 " pdb=" OP2 U T 2 " pdb=" O5' U T 2 " both_signs ideal model delta sigma weight residual True 2.41 2.86 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C3' GTP T 101 " pdb=" C2' GTP T 101 " pdb=" C4' GTP T 101 " pdb=" O3' GTP T 101 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1898 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 223 " -0.045 2.00e-02 2.50e+03 3.02e-02 1.60e+01 pdb=" CG PHE C 223 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 223 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE C 223 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE C 223 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 223 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 223 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 223 " -0.036 2.00e-02 2.50e+03 2.28e-02 9.08e+00 pdb=" CG PHE D 223 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE D 223 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE D 223 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE D 223 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 223 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 223 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 223 " 0.036 2.00e-02 2.50e+03 2.28e-02 9.07e+00 pdb=" CG PHE B 223 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 223 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 223 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE B 223 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 223 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 223 " 0.029 2.00e-02 2.50e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 65 2.60 - 3.17: 9534 3.17 - 3.75: 19294 3.75 - 4.32: 27785 4.32 - 4.90: 42544 Nonbonded interactions: 99222 Sorted by model distance: nonbonded pdb=" OP1 U T 11 " pdb="MG MG T 102 " model vdw 2.021 2.170 nonbonded pdb=" NE2 GLN A 115 " pdb=" OD1 ASP A 119 " model vdw 2.331 3.120 nonbonded pdb=" OH TYR F 135 " pdb=" OP1 A T 42 " model vdw 2.388 3.040 nonbonded pdb=" NH2 ARG F 102 " pdb=" O PRO F 109 " model vdw 2.403 3.120 nonbonded pdb=" OE2 GLU A 68 " pdb=" NH2 ARG A 130 " model vdw 2.409 3.120 ... (remaining 99217 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' selection = chain 'C' selection = chain 'D' } 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: 18.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 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 : 0.008 0.076 11543 Z= 0.499 Angle : 0.906 11.062 15948 Z= 0.553 Chirality : 0.067 0.518 1901 Planarity : 0.007 0.067 1826 Dihedral : 17.051 178.479 4694 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.50 (0.23), residues: 1292 helix: 1.84 (0.21), residues: 630 sheet: -0.16 (0.33), residues: 201 loop : 0.51 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG C 130 TYR 0.016 0.004 TYR F 262 PHE 0.045 0.007 PHE C 223 TRP 0.022 0.005 TRP F 183 HIS 0.012 0.003 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00791 (11542) covalent geometry : angle 0.90617 (15948) hydrogen bonds : bond 0.19401 ( 571) hydrogen bonds : angle 7.20900 ( 1610) Misc. bond : bond 0.06063 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.438 Fit side-chains REVERT: A 105 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8423 (mptt) REVERT: D 215 ASN cc_start: 0.6687 (t0) cc_final: 0.6485 (t0) REVERT: F 149 LYS cc_start: 0.7240 (mttt) cc_final: 0.6947 (tmmm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.9082 time to fit residues: 162.3642 Evaluate side-chains 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 56 ASN F 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097169 restraints weight = 10189.504| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.77 r_work: 0.3089 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11543 Z= 0.151 Angle : 0.574 6.559 15948 Z= 0.298 Chirality : 0.042 0.185 1901 Planarity : 0.004 0.037 1826 Dihedral : 17.291 176.636 2415 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.68 % Allowed : 6.45 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.95 (0.24), residues: 1292 helix: 2.47 (0.21), residues: 609 sheet: -0.51 (0.32), residues: 193 loop : 0.68 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.009 0.001 TYR F 135 PHE 0.015 0.002 PHE C 126 TRP 0.010 0.001 TRP F 183 HIS 0.005 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00322 (11542) covalent geometry : angle 0.57372 (15948) hydrogen bonds : bond 0.05415 ( 571) hydrogen bonds : angle 5.28536 ( 1610) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.534 Fit side-chains REVERT: A 105 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8431 (mptt) outliers start: 7 outliers final: 3 residues processed: 155 average time/residue: 0.8622 time to fit residues: 141.0748 Evaluate side-chains 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095596 restraints weight = 10297.465| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 0.77 r_work: 0.3065 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11543 Z= 0.182 Angle : 0.606 6.808 15948 Z= 0.315 Chirality : 0.043 0.238 1901 Planarity : 0.005 0.050 1826 Dihedral : 17.290 174.775 2415 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.08 % Allowed : 7.33 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.66 (0.23), residues: 1292 helix: 2.25 (0.21), residues: 615 sheet: -0.73 (0.32), residues: 199 loop : 0.55 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 106 TYR 0.012 0.002 TYR F 135 PHE 0.017 0.002 PHE B 223 TRP 0.010 0.001 TRP F 183 HIS 0.004 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00390 (11542) covalent geometry : angle 0.60603 (15948) hydrogen bonds : bond 0.05693 ( 571) hydrogen bonds : angle 5.32314 ( 1610) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.395 Fit side-chains REVERT: D 205 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5885 (pp) REVERT: F 217 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7711 (tpm-80) outliers start: 11 outliers final: 4 residues processed: 147 average time/residue: 0.8849 time to fit residues: 137.2213 Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096759 restraints weight = 10360.349| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.77 r_work: 0.3085 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11543 Z= 0.149 Angle : 0.566 6.513 15948 Z= 0.292 Chirality : 0.041 0.182 1901 Planarity : 0.004 0.038 1826 Dihedral : 17.141 175.710 2415 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.98 % Allowed : 8.50 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.78 (0.23), residues: 1292 helix: 2.42 (0.21), residues: 609 sheet: -0.79 (0.32), residues: 193 loop : 0.56 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 147 TYR 0.011 0.001 TYR F 135 PHE 0.015 0.002 PHE B 223 TRP 0.009 0.001 TRP F 183 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00318 (11542) covalent geometry : angle 0.56580 (15948) hydrogen bonds : bond 0.05039 ( 571) hydrogen bonds : angle 5.14192 ( 1610) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.334 Fit side-chains REVERT: F 217 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7681 (tpm-80) outliers start: 10 outliers final: 4 residues processed: 150 average time/residue: 0.8449 time to fit residues: 133.8766 Evaluate side-chains 142 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 0.9990 chunk 112 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095228 restraints weight = 10278.322| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 0.76 r_work: 0.3058 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11543 Z= 0.201 Angle : 0.630 6.809 15948 Z= 0.326 Chirality : 0.044 0.267 1901 Planarity : 0.005 0.055 1826 Dihedral : 17.245 174.927 2415 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.27 % Allowed : 8.50 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.58 (0.23), residues: 1292 helix: 2.20 (0.21), residues: 604 sheet: -0.82 (0.32), residues: 199 loop : 0.55 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 130 TYR 0.014 0.002 TYR F 135 PHE 0.019 0.002 PHE B 223 TRP 0.010 0.002 TRP F 183 HIS 0.004 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00432 (11542) covalent geometry : angle 0.62981 (15948) hydrogen bonds : bond 0.05744 ( 571) hydrogen bonds : angle 5.33206 ( 1610) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.405 Fit side-chains REVERT: F 217 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7721 (tpm-80) outliers start: 13 outliers final: 4 residues processed: 146 average time/residue: 0.8186 time to fit residues: 126.4380 Evaluate side-chains 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 70 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 15 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096306 restraints weight = 10378.688| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.77 r_work: 0.3077 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11543 Z= 0.162 Angle : 0.588 7.673 15948 Z= 0.302 Chirality : 0.042 0.195 1901 Planarity : 0.005 0.042 1826 Dihedral : 17.188 175.850 2415 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.88 % Allowed : 8.90 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.23), residues: 1292 helix: 2.31 (0.21), residues: 604 sheet: -0.81 (0.32), residues: 193 loop : 0.64 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.011 0.002 TYR F 135 PHE 0.016 0.002 PHE B 223 TRP 0.009 0.001 TRP F 183 HIS 0.003 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00346 (11542) covalent geometry : angle 0.58819 (15948) hydrogen bonds : bond 0.05198 ( 571) hydrogen bonds : angle 5.18698 ( 1610) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.402 Fit side-chains REVERT: F 217 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7703 (tpm-80) outliers start: 9 outliers final: 3 residues processed: 147 average time/residue: 0.8355 time to fit residues: 129.8411 Evaluate side-chains 135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 88 optimal weight: 0.0030 chunk 53 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097414 restraints weight = 10353.429| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.77 r_work: 0.3097 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11543 Z= 0.135 Angle : 0.578 18.282 15948 Z= 0.289 Chirality : 0.041 0.167 1901 Planarity : 0.004 0.036 1826 Dihedral : 17.091 175.763 2415 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.59 % Allowed : 9.29 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.81 (0.24), residues: 1292 helix: 2.45 (0.21), residues: 604 sheet: -0.73 (0.32), residues: 203 loop : 0.61 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 147 TYR 0.010 0.001 TYR F 135 PHE 0.014 0.002 PHE B 223 TRP 0.008 0.001 TRP F 183 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00289 (11542) covalent geometry : angle 0.57837 (15948) hydrogen bonds : bond 0.04742 ( 571) hydrogen bonds : angle 5.05849 ( 1610) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.398 Fit side-chains REVERT: F 217 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7655 (tpm-80) outliers start: 6 outliers final: 3 residues processed: 144 average time/residue: 0.7991 time to fit residues: 121.9744 Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095444 restraints weight = 10274.303| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.76 r_work: 0.3062 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11543 Z= 0.198 Angle : 0.645 15.606 15948 Z= 0.328 Chirality : 0.044 0.256 1901 Planarity : 0.005 0.051 1826 Dihedral : 17.192 174.981 2415 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.59 % Allowed : 9.97 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.62 (0.23), residues: 1292 helix: 2.21 (0.21), residues: 604 sheet: -0.82 (0.32), residues: 199 loop : 0.61 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.013 0.002 TYR F 135 PHE 0.019 0.002 PHE B 223 TRP 0.010 0.002 TRP F 183 HIS 0.005 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00427 (11542) covalent geometry : angle 0.64534 (15948) hydrogen bonds : bond 0.05651 ( 571) hydrogen bonds : angle 5.29495 ( 1610) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.401 Fit side-chains REVERT: F 217 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7706 (tpm-80) outliers start: 6 outliers final: 4 residues processed: 136 average time/residue: 0.8520 time to fit residues: 122.5048 Evaluate side-chains 133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 328 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095681 restraints weight = 10272.826| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 0.76 r_work: 0.3064 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11543 Z= 0.190 Angle : 0.639 14.510 15948 Z= 0.326 Chirality : 0.043 0.243 1901 Planarity : 0.005 0.051 1826 Dihedral : 17.200 175.510 2415 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.59 % Allowed : 10.26 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.61 (0.23), residues: 1292 helix: 2.24 (0.21), residues: 598 sheet: -0.82 (0.32), residues: 199 loop : 0.58 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.013 0.002 TYR F 135 PHE 0.018 0.002 PHE B 223 TRP 0.009 0.002 TRP F 183 HIS 0.004 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00411 (11542) covalent geometry : angle 0.63914 (15948) hydrogen bonds : bond 0.05555 ( 571) hydrogen bonds : angle 5.28068 ( 1610) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.352 Fit side-chains REVERT: F 217 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7695 (tpm-80) outliers start: 6 outliers final: 4 residues processed: 134 average time/residue: 0.8388 time to fit residues: 118.8007 Evaluate side-chains 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 38 optimal weight: 0.0060 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096507 restraints weight = 10349.645| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 0.76 r_work: 0.3080 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11543 Z= 0.158 Angle : 0.606 13.681 15948 Z= 0.307 Chirality : 0.042 0.191 1901 Planarity : 0.005 0.041 1826 Dihedral : 17.140 175.863 2415 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.68 % Allowed : 10.26 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.23), residues: 1292 helix: 2.32 (0.21), residues: 598 sheet: -0.82 (0.32), residues: 193 loop : 0.62 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.011 0.002 TYR F 135 PHE 0.016 0.002 PHE B 223 TRP 0.009 0.001 TRP F 369 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00342 (11542) covalent geometry : angle 0.60638 (15948) hydrogen bonds : bond 0.05114 ( 571) hydrogen bonds : angle 5.17112 ( 1610) Misc. bond : bond 0.00055 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.413 Fit side-chains REVERT: F 217 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7697 (tpm-80) outliers start: 7 outliers final: 4 residues processed: 143 average time/residue: 0.8629 time to fit residues: 130.3985 Evaluate side-chains 139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095597 restraints weight = 10406.711| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 0.76 r_work: 0.3065 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11543 Z= 0.188 Angle : 0.639 13.128 15948 Z= 0.327 Chirality : 0.043 0.242 1901 Planarity : 0.005 0.051 1826 Dihedral : 17.187 175.192 2415 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.59 % Allowed : 10.36 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.51 (0.23), residues: 1292 helix: 2.10 (0.21), residues: 610 sheet: -0.83 (0.32), residues: 199 loop : 0.55 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 147 TYR 0.012 0.002 TYR F 135 PHE 0.018 0.002 PHE B 223 TRP 0.010 0.002 TRP F 183 HIS 0.004 0.001 HIS F 111 Details of bonding type rmsd covalent geometry : bond 0.00407 (11542) covalent geometry : angle 0.63906 (15948) hydrogen bonds : bond 0.05564 ( 571) hydrogen bonds : angle 5.27969 ( 1610) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7276.08 seconds wall clock time: 124 minutes 16.66 seconds (7456.66 seconds total)