Starting phenix.real_space_refine on Tue May 13 23:48:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gch_51230/05_2025/9gch_51230.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gch_51230/05_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_51230/05_2025/9gch_51230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gch_51230/05_2025/9gch_51230.map" model { file = "/net/cci-nas-00/data/ceres_data/9gch_51230/05_2025/9gch_51230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gch_51230/05_2025/9gch_51230.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.51, per 1000 atoms: 0.94 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: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.23 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: 3.40 Time building geometry restraints manager: 3.31 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: 13.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 34.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.005 TRP F 183 HIS 0.012 0.003 HIS B 109 PHE 0.045 0.007 PHE C 223 TYR 0.016 0.004 TYR F 262 ARG 0.023 0.003 ARG C 130 Details of bonding type rmsd hydrogen bonds : bond 0.19401 ( 571) hydrogen bonds : angle 7.20900 ( 1610) covalent geometry : bond 0.00791 (11542) covalent geometry : angle 0.90617 (15948) 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 : 1.062 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: 1.7777 time to fit residues: 319.0372 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 : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.130379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096052 restraints weight = 10141.559| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 0.77 r_work: 0.3066 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11543 Z= 0.186 Angle : 0.617 6.702 15948 Z= 0.321 Chirality : 0.043 0.230 1901 Planarity : 0.005 0.052 1826 Dihedral : 17.395 175.841 2415 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.78 % Allowed : 6.65 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1292 helix: 2.37 (0.21), residues: 604 sheet: -0.56 (0.32), residues: 199 loop : 0.68 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 183 HIS 0.004 0.001 HIS F 242 PHE 0.017 0.002 PHE B 223 TYR 0.011 0.002 TYR F 135 ARG 0.003 0.001 ARG F 106 Details of bonding type rmsd hydrogen bonds : bond 0.05909 ( 571) hydrogen bonds : angle 5.42256 ( 1610) covalent geometry : bond 0.00400 (11542) covalent geometry : angle 0.61655 (15948) Misc. bond : bond 0.00101 ( 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 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.103 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 145 average time/residue: 1.6452 time to fit residues: 253.2762 Evaluate side-chains 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 48 GLU 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 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097894 restraints weight = 10327.835| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 0.77 r_work: 0.3104 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1428 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= 0.130 Angle : 0.540 6.581 15948 Z= 0.277 Chirality : 0.041 0.157 1901 Planarity : 0.004 0.033 1826 Dihedral : 17.157 175.624 2415 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.98 % Allowed : 7.14 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1292 helix: 2.49 (0.21), residues: 609 sheet: -0.64 (0.31), residues: 211 loop : 0.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 183 HIS 0.002 0.001 HIS B 109 PHE 0.013 0.002 PHE B 223 TYR 0.010 0.001 TYR F 135 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 571) hydrogen bonds : angle 5.09494 ( 1610) covalent geometry : bond 0.00277 (11542) covalent geometry : angle 0.53994 (15948) Misc. bond : bond 0.00074 ( 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 161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.089 Fit side-chains REVERT: A 105 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8455 (mptt) REVERT: F 217 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (tpm-80) outliers start: 10 outliers final: 3 residues processed: 155 average time/residue: 1.6892 time to fit residues: 276.9558 Evaluate side-chains 131 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.130203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096260 restraints weight = 10258.483| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 0.76 r_work: 0.3075 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11543 Z= 0.164 Angle : 0.589 6.557 15948 Z= 0.303 Chirality : 0.042 0.207 1901 Planarity : 0.005 0.045 1826 Dihedral : 17.156 175.099 2415 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.88 % Allowed : 8.31 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1292 helix: 2.34 (0.21), residues: 609 sheet: -0.77 (0.32), residues: 199 loop : 0.55 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 183 HIS 0.003 0.001 HIS B 109 PHE 0.016 0.002 PHE B 223 TYR 0.012 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 571) hydrogen bonds : angle 5.20854 ( 1610) covalent geometry : bond 0.00352 (11542) covalent geometry : angle 0.58949 (15948) 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 144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.230 Fit side-chains REVERT: F 217 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7709 (tpm-80) outliers start: 9 outliers final: 4 residues processed: 139 average time/residue: 1.6916 time to fit residues: 249.3452 Evaluate side-chains 127 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 123 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 92 optimal weight: 0.2980 chunk 71 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.131178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097353 restraints weight = 10267.454| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.77 r_work: 0.3096 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 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 0.047 11543 Z= 0.139 Angle : 0.555 7.142 15948 Z= 0.284 Chirality : 0.041 0.171 1901 Planarity : 0.004 0.034 1826 Dihedral : 17.079 175.747 2415 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 8.90 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1292 helix: 2.44 (0.21), residues: 604 sheet: -0.70 (0.32), residues: 203 loop : 0.58 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.003 0.001 HIS B 109 PHE 0.014 0.002 PHE B 223 TYR 0.011 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 571) hydrogen bonds : angle 5.08118 ( 1610) covalent geometry : bond 0.00296 (11542) covalent geometry : angle 0.55472 (15948) Misc. bond : bond 0.00054 ( 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 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.105 Fit side-chains REVERT: F 217 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7659 (tpm-80) outliers start: 8 outliers final: 3 residues processed: 137 average time/residue: 1.6470 time to fit residues: 239.7305 Evaluate side-chains 129 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.129753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095805 restraints weight = 10397.977| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 0.77 r_work: 0.3069 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11543 Z= 0.180 Angle : 0.607 8.521 15948 Z= 0.312 Chirality : 0.042 0.233 1901 Planarity : 0.005 0.049 1826 Dihedral : 17.205 175.071 2415 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.88 % Allowed : 8.80 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1292 helix: 2.33 (0.21), residues: 598 sheet: -0.81 (0.32), residues: 199 loop : 0.60 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 183 HIS 0.004 0.001 HIS F 111 PHE 0.018 0.002 PHE B 223 TYR 0.013 0.002 TYR F 135 ARG 0.004 0.001 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 571) hydrogen bonds : angle 5.25017 ( 1610) covalent geometry : bond 0.00387 (11542) covalent geometry : angle 0.60660 (15948) Misc. bond : bond 0.00060 ( 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 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.185 Fit side-chains REVERT: F 217 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7722 (tpm-80) outliers start: 9 outliers final: 4 residues processed: 137 average time/residue: 1.6650 time to fit residues: 242.5416 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096767 restraints weight = 10438.373| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.77 r_work: 0.3084 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11543 Z= 0.149 Angle : 0.590 17.560 15948 Z= 0.297 Chirality : 0.042 0.181 1901 Planarity : 0.004 0.038 1826 Dihedral : 17.107 175.944 2415 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 8.90 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1292 helix: 2.36 (0.21), residues: 609 sheet: -0.82 (0.32), residues: 193 loop : 0.59 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.003 0.001 HIS B 109 PHE 0.015 0.002 PHE B 223 TYR 0.011 0.001 TYR F 135 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 571) hydrogen bonds : angle 5.12323 ( 1610) covalent geometry : bond 0.00321 (11542) covalent geometry : angle 0.59013 (15948) Misc. bond : bond 0.00054 ( 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 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.264 Fit side-chains REVERT: F 217 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7681 (tpm-80) outliers start: 8 outliers final: 3 residues processed: 135 average time/residue: 1.7536 time to fit residues: 252.5485 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 110 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098192 restraints weight = 10376.724| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.76 r_work: 0.3109 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11543 Z= 0.126 Angle : 0.561 14.221 15948 Z= 0.281 Chirality : 0.040 0.154 1901 Planarity : 0.004 0.037 1826 Dihedral : 16.999 175.795 2415 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.59 % Allowed : 9.58 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1292 helix: 2.49 (0.21), residues: 604 sheet: -0.76 (0.31), residues: 211 loop : 0.67 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.002 0.001 HIS B 109 PHE 0.013 0.002 PHE B 223 TYR 0.009 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 571) hydrogen bonds : angle 4.99414 ( 1610) covalent geometry : bond 0.00272 (11542) covalent geometry : angle 0.56062 (15948) Misc. bond : bond 0.00045 ( 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 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.274 Fit side-chains REVERT: F 217 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7645 (tpm-80) outliers start: 6 outliers final: 3 residues processed: 138 average time/residue: 1.6112 time to fit residues: 236.6524 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 : 1.092 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096422 restraints weight = 10370.917| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 0.77 r_work: 0.3079 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11543 Z= 0.164 Angle : 0.610 13.067 15948 Z= 0.309 Chirality : 0.042 0.205 1901 Planarity : 0.005 0.041 1826 Dihedral : 17.075 175.281 2415 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.39 % Allowed : 9.97 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1292 helix: 2.25 (0.21), residues: 610 sheet: -0.80 (0.32), residues: 193 loop : 0.60 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.003 0.001 HIS B 109 PHE 0.017 0.002 PHE B 223 TYR 0.012 0.002 TYR F 135 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 571) hydrogen bonds : angle 5.16611 ( 1610) covalent geometry : bond 0.00354 (11542) covalent geometry : angle 0.60959 (15948) Misc. bond : bond 0.00038 ( 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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 1.081 Fit side-chains REVERT: F 217 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7687 (tpm-80) outliers start: 4 outliers final: 3 residues processed: 132 average time/residue: 1.6811 time to fit residues: 235.3076 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN C 56 ASN D 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097869 restraints weight = 10379.559| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.77 r_work: 0.3105 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11543 Z= 0.133 Angle : 0.573 12.434 15948 Z= 0.288 Chirality : 0.041 0.160 1901 Planarity : 0.004 0.039 1826 Dihedral : 17.014 175.996 2415 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.49 % Allowed : 9.78 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1292 helix: 2.40 (0.21), residues: 609 sheet: -0.73 (0.32), residues: 203 loop : 0.58 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 183 HIS 0.002 0.001 HIS B 109 PHE 0.013 0.002 PHE B 223 TYR 0.010 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 571) hydrogen bonds : angle 5.03504 ( 1610) covalent geometry : bond 0.00288 (11542) covalent geometry : angle 0.57300 (15948) Misc. bond : bond 0.00042 ( 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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.245 Fit side-chains REVERT: F 217 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7653 (tpm-80) outliers start: 5 outliers final: 3 residues processed: 132 average time/residue: 1.6563 time to fit residues: 233.7329 Evaluate side-chains 136 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 260 GLN C 56 ASN D 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094982 restraints weight = 10293.264| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.77 r_work: 0.3054 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11543 Z= 0.231 Angle : 0.681 12.186 15948 Z= 0.349 Chirality : 0.045 0.309 1901 Planarity : 0.005 0.061 1826 Dihedral : 17.190 174.759 2415 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.59 % Allowed : 10.07 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1292 helix: 2.06 (0.21), residues: 610 sheet: -0.78 (0.32), residues: 199 loop : 0.54 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 183 HIS 0.006 0.002 HIS F 111 PHE 0.021 0.003 PHE B 223 TYR 0.016 0.002 TYR F 135 ARG 0.004 0.001 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05955 ( 571) hydrogen bonds : angle 5.37813 ( 1610) covalent geometry : bond 0.00499 (11542) covalent geometry : angle 0.68104 (15948) Misc. bond : bond 0.00050 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13628.53 seconds wall clock time: 236 minutes 42.04 seconds (14202.04 seconds total)