Starting phenix.real_space_refine on Tue Jul 29 07:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gch_51230/07_2025/9gch_51230.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gch_51230/07_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_51230/07_2025/9gch_51230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2025/9gch_51230.map" model { file = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_2025/9gch_51230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gch_51230/07_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-5711/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: 10.57, 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 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: 3.81 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: 3.49 Time building geometry restraints manager: 3.20 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: 28.210 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.460 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: 0.010 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.790 ------------------------------------------------------------------------------- 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 : 1.101 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: 1.8731 time to fit residues: 335.8642 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 : 1.107 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096093 restraints weight = 10141.559| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 0.77 r_work: 0.3068 rms_B_bonded: 1.33 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 : 1.315 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 145 average time/residue: 1.7287 time to fit residues: 265.8062 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 : 1.236 ------------------------------------------------------------------------------- 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: 0.0980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 overall best weight: 0.2278 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.133470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099847 restraints weight = 10403.945| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.77 r_work: 0.3136 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11543 Z= 0.111 Angle : 0.513 6.479 15948 Z= 0.262 Chirality : 0.040 0.136 1901 Planarity : 0.004 0.034 1826 Dihedral : 17.114 175.960 2415 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.78 % Allowed : 7.23 % Favored : 91.98 % 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: 1.98 (0.24), residues: 1292 helix: 2.58 (0.21), residues: 609 sheet: -0.67 (0.31), residues: 213 loop : 0.73 (0.29), residues: 470 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 0.012 0.002 PHE B 126 TYR 0.009 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 571) hydrogen bonds : angle 4.97393 ( 1610) covalent geometry : bond 0.00234 (11542) covalent geometry : angle 0.51289 (15948) Misc. bond : bond 0.00075 ( 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 166 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.127 Fit side-chains REVERT: A 105 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8449 (mptt) REVERT: C 16 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (p) REVERT: D 16 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8609 (p) outliers start: 8 outliers final: 1 residues processed: 161 average time/residue: 2.1680 time to fit residues: 369.0188 Evaluate side-chains 144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain F residue 133 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 96 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN F 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097001 restraints weight = 10273.034| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 0.76 r_work: 0.3087 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1426 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= 0.147 Angle : 0.570 6.488 15948 Z= 0.292 Chirality : 0.041 0.181 1901 Planarity : 0.004 0.039 1826 Dihedral : 17.087 175.159 2415 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.88 % Allowed : 8.70 % Favored : 90.42 % 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: 1.83 (0.23), residues: 1292 helix: 2.44 (0.21), residues: 609 sheet: -0.75 (0.32), residues: 193 loop : 0.60 (0.29), residues: 490 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 0.015 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 0.05035 ( 571) hydrogen bonds : angle 5.11849 ( 1610) covalent geometry : bond 0.00313 (11542) covalent geometry : angle 0.56966 (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 147 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.085 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 144 average time/residue: 1.7736 time to fit residues: 270.5396 Evaluate side-chains 135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN F 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096913 restraints weight = 10260.953| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 0.76 r_work: 0.3088 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work: 0.2839 rms_B_bonded: 4.97 restraints_weight: 0.1250 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1482 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= 0.151 Angle : 0.574 6.890 15948 Z= 0.294 Chirality : 0.041 0.190 1901 Planarity : 0.004 0.040 1826 Dihedral : 17.078 175.508 2415 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 (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: 1.75 (0.23), residues: 1292 helix: 2.38 (0.21), residues: 610 sheet: -0.79 (0.32), residues: 193 loop : 0.55 (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 0.016 0.002 PHE B 223 TYR 0.012 0.001 TYR F 135 ARG 0.002 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 571) hydrogen bonds : angle 5.13411 ( 1610) covalent geometry : bond 0.00324 (11542) covalent geometry : angle 0.57441 (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 143 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.154 Fit side-chains REVERT: F 152 MET cc_start: 0.6466 (tmm) cc_final: 0.5404 (pp-130) outliers start: 6 outliers final: 4 residues processed: 141 average time/residue: 1.7620 time to fit residues: 263.3640 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 : 1.184 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 126 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN F 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096516 restraints weight = 10411.814| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 0.77 r_work: 0.3081 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1517 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= 0.159 Angle : 0.585 8.657 15948 Z= 0.300 Chirality : 0.042 0.199 1901 Planarity : 0.005 0.042 1826 Dihedral : 17.153 178.577 2415 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.78 % Allowed : 9.09 % 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 (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: 1.75 (0.23), residues: 1292 helix: 2.36 (0.21), residues: 609 sheet: -0.81 (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 F 111 PHE 0.016 0.002 PHE B 223 TYR 0.012 0.002 TYR F 135 ARG 0.002 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 571) hydrogen bonds : angle 5.17427 ( 1610) covalent geometry : bond 0.00341 (11542) covalent geometry : angle 0.58491 (15948) Misc. bond : bond 0.00053 ( 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 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.133 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 138 average time/residue: 2.1963 time to fit residues: 322.4427 Evaluate side-chains 135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 F 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097451 restraints weight = 10459.580| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.77 r_work: 0.3097 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11543 Z= 0.139 Angle : 0.564 8.148 15948 Z= 0.287 Chirality : 0.041 0.171 1901 Planarity : 0.004 0.035 1826 Dihedral : 17.022 175.873 2415 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 9.38 % 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: 1.79 (0.23), residues: 1292 helix: 2.43 (0.21), residues: 609 sheet: -0.72 (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 0.003 0.001 HIS B 109 PHE 0.014 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 0.04795 ( 571) hydrogen bonds : angle 5.06869 ( 1610) covalent geometry : bond 0.00299 (11542) covalent geometry : angle 0.56355 (15948) Misc. bond : bond 0.00048 ( 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 140 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.022 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 138 average time/residue: 1.6241 time to fit residues: 238.7360 Evaluate side-chains 131 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 F 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096566 restraints weight = 10317.536| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.76 r_work: 0.3082 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1573 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= 0.159 Angle : 0.610 18.569 15948 Z= 0.306 Chirality : 0.042 0.198 1901 Planarity : 0.005 0.041 1826 Dihedral : 17.063 175.344 2415 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.76 (0.23), residues: 1292 helix: 2.39 (0.21), residues: 604 sheet: -0.80 (0.32), residues: 193 loop : 0.60 (0.29), residues: 495 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 0.016 0.002 PHE B 223 TYR 0.011 0.002 TYR F 135 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 571) hydrogen bonds : angle 5.15191 ( 1610) covalent geometry : bond 0.00342 (11542) covalent geometry : angle 0.61028 (15948) Misc. bond : bond 0.00041 ( 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: 5 poor density : 133 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 136 average time/residue: 1.7197 time to fit residues: 247.9094 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 : 1.069 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 F 370 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095586 restraints weight = 10366.495| |-----------------------------------------------------------------------------| 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: 0.2980 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11543 Z= 0.193 Angle : 0.645 15.968 15948 Z= 0.328 Chirality : 0.044 0.252 1901 Planarity : 0.005 0.052 1826 Dihedral : 17.169 175.076 2415 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.49 % Allowed : 9.97 % Favored : 89.54 % 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: 1.58 (0.23), residues: 1292 helix: 2.18 (0.21), residues: 610 sheet: -0.81 (0.32), residues: 199 loop : 0.56 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 183 HIS 0.004 0.001 HIS F 111 PHE 0.019 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 0.05620 ( 571) hydrogen bonds : angle 5.29395 ( 1610) covalent geometry : bond 0.00417 (11542) covalent geometry : angle 0.64468 (15948) Misc. bond : bond 0.00045 ( 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 139 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 2.338 Fit side-chains REVERT: A 105 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8470 (mptt) outliers start: 5 outliers final: 4 residues processed: 137 average time/residue: 1.7291 time to fit residues: 252.8299 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 : 1.173 ------------------------------------------------------------------------------- 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 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097454 restraints weight = 10383.791| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.77 r_work: 0.3099 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1647 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= 0.139 Angle : 0.589 14.541 15948 Z= 0.296 Chirality : 0.041 0.171 1901 Planarity : 0.004 0.035 1826 Dihedral : 17.067 176.046 2415 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.39 % Allowed : 10.07 % Favored : 89.54 % 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: 1.75 (0.24), residues: 1292 helix: 2.37 (0.21), residues: 609 sheet: -0.74 (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 0.003 0.001 HIS B 109 PHE 0.014 0.002 PHE C 126 TYR 0.010 0.001 TYR F 135 ARG 0.003 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 571) hydrogen bonds : angle 5.08245 ( 1610) covalent geometry : bond 0.00301 (11542) covalent geometry : angle 0.58857 (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 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 1.053 Fit side-chains REVERT: F 152 MET cc_start: 0.6249 (tmm) cc_final: 0.5017 (pp-130) outliers start: 4 outliers final: 3 residues processed: 140 average time/residue: 1.6516 time to fit residues: 245.9212 Evaluate side-chains 137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 105 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096218 restraints weight = 10335.684| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 0.76 r_work: 0.3076 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11543 Z= 0.171 Angle : 0.626 13.913 15948 Z= 0.318 Chirality : 0.043 0.215 1901 Planarity : 0.005 0.044 1826 Dihedral : 17.113 175.157 2415 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.49 % Allowed : 10.26 % Favored : 89.25 % 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: 2.26 (0.21), residues: 604 sheet: -0.81 (0.32), residues: 193 loop : 0.61 (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 0.017 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 0.05296 ( 571) hydrogen bonds : angle 5.21183 ( 1610) covalent geometry : bond 0.00368 (11542) covalent geometry : angle 0.62601 (15948) Misc. bond : bond 0.00036 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16196.88 seconds wall clock time: 286 minutes 2.18 seconds (17162.18 seconds total)