Starting phenix.real_space_refine on Fri Jul 3 08:41:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2026/7xjg_33226.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 216 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7594 2.51 5 N 2367 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13167 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 933 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2490 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.25 Number of scatterers: 13167 At special positions: 0 Unit cell: (96.9, 122.4, 161.5, 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 34 16.00 P 216 15.00 Mg 2 11.99 O 2954 8.00 N 2367 7.00 C 7594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 527.6 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 60.1% alpha, 9.8% beta 68 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.576A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.748A pdb=" N MET A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.616A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 removed outlier: 3.946A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.557A pdb=" N SER A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.550A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 removed outlier: 3.598A pdb=" N GLY A 224 " --> pdb=" O PRO A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.726A pdb=" N GLN C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.509A pdb=" N LEU C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.585A pdb=" N LEU C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.888A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 removed outlier: 3.510A pdb=" N MET B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.749A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.848A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 186 Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.600A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.778A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.759A pdb=" N LEU J 49 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 100 through 111 Processing helix chain 'J' and resid 125 through 129 Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 138 through 147 Processing helix chain 'J' and resid 155 through 162 removed outlier: 3.768A pdb=" N LEU J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.742A pdb=" N ARG J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 190 Processing helix chain 'J' and resid 202 through 213 Proline residue: J 208 - end of helix Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 233 through 235 No H-bonds generated for 'chain 'J' and resid 233 through 235' Processing helix chain 'J' and resid 236 through 250 removed outlier: 3.757A pdb=" N VAL J 240 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG J 241 " --> pdb=" O LYS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 274 Processing helix chain 'J' and resid 275 through 292 removed outlier: 3.814A pdb=" N LEU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG J 292 " --> pdb=" O ASN J 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.604A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 4.570A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA9, first strand: chain 'J' and resid 59 through 62 removed outlier: 6.601A pdb=" N ILE J 30 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N PHE J 62 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE J 32 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE J 94 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE J 123 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU J 96 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU J 152 " --> pdb=" O LEU J 120 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS J 122 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 253 through 256 449 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1964 1.33 - 1.45: 4683 1.45 - 1.57: 6743 1.57 - 1.69: 422 1.69 - 1.81: 50 Bond restraints: 13862 Sorted by residual: bond pdb=" CA SER B 218 " pdb=" CB SER B 218 " ideal model delta sigma weight residual 1.532 1.473 0.059 1.53e-02 4.27e+03 1.50e+01 bond pdb=" C3' DA D 8 " pdb=" C2' DA D 8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA G 8 " pdb=" C2' DA G 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C3' DA G 9 " pdb=" C2' DA G 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.19e+00 bond pdb=" C3' DA D 11 " pdb=" C2' DA D 11 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.17e+00 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 19080 2.06 - 4.13: 522 4.13 - 6.19: 55 6.19 - 8.26: 4 8.26 - 10.32: 4 Bond angle restraints: 19665 Sorted by residual: angle pdb=" C GLU B 59 " pdb=" CA GLU B 59 " pdb=" CB GLU B 59 " ideal model delta sigma weight residual 116.54 109.75 6.79 1.15e+00 7.56e-01 3.49e+01 angle pdb=" O4' DT D 82 " pdb=" C4' DT D 82 " pdb=" C3' DT D 82 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 angle pdb=" C ILE B 219 " pdb=" N ILE B 220 " pdb=" CA ILE B 220 " ideal model delta sigma weight residual 122.13 111.81 10.32 1.85e+00 2.92e-01 3.11e+01 angle pdb=" O4' DT G 82 " pdb=" C4' DT G 82 " pdb=" C3' DT G 82 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" O4' DC D 83 " pdb=" C4' DC D 83 " pdb=" C3' DC D 83 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7283 35.95 - 71.89: 609 71.89 - 107.84: 11 107.84 - 143.78: 8 143.78 - 179.73: 15 Dihedral angle restraints: 7926 sinusoidal: 4799 harmonic: 3127 Sorted by residual: dihedral pdb=" O4' U H 68 " pdb=" C1' U H 68 " pdb=" N1 U H 68 " pdb=" C2 U H 68 " ideal model delta sinusoidal sigma weight residual 200.00 20.41 179.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual 200.00 53.56 146.44 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' C H 65 " pdb=" C1' C H 65 " pdb=" N1 C H 65 " pdb=" C2 C H 65 " ideal model delta sinusoidal sigma weight residual 200.00 63.30 136.70 1 1.50e+01 4.44e-03 7.37e+01 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1876 0.056 - 0.112: 350 0.112 - 0.168: 77 0.168 - 0.224: 14 0.224 - 0.280: 2 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C3' DC G 3 " pdb=" C4' DC G 3 " pdb=" O3' DC G 3 " pdb=" C2' DC G 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" P G F 1 " pdb=" OP1 G F 1 " pdb=" OP2 G F 1 " pdb=" O5' G F 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA TYR A 195 " pdb=" N TYR A 195 " pdb=" C TYR A 195 " pdb=" CB TYR A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2316 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 223 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" CD GLU J 223 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU J 223 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU J 223 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 302 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO J 303 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 303 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 303 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 125 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.033 5.00e-02 4.00e+02 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 60 2.55 - 3.14: 9033 3.14 - 3.72: 21354 3.72 - 4.31: 31367 4.31 - 4.90: 47292 Nonbonded interactions: 109106 Sorted by model distance: nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 1.962 3.040 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.010 3.120 nonbonded pdb=" N2 G E 20 " pdb=" O2 U E 41 " model vdw 2.209 3.120 nonbonded pdb=" OP1 DG D 14 " pdb=" NH2 ARG J 276 " model vdw 2.211 3.120 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.234 3.120 ... (remaining 109101 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' } ncs_group { reference = (chain 'D' and (resid 1 through 19 or resid 66 through 85)) selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 2.960 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.240 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.005 0.059 13862 Z= 0.361 Angle : 0.747 10.322 19665 Z= 0.501 Chirality : 0.049 0.280 2319 Planarity : 0.005 0.060 1697 Dihedral : 22.358 179.725 5906 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 26.38 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1054 helix: 0.43 (0.23), residues: 547 sheet: 1.77 (0.53), residues: 87 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 31 TYR 0.024 0.002 TYR B 184 PHE 0.015 0.002 PHE B 96 TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.36 (13862) covalent geometry : angle 0.74657 / 0.50 (19665) hydrogen bonds : bond 0.16129 / 10.74 ( 607) hydrogen bonds : angle 5.30362 / 3.72 ( 1589) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.408 Fit side-chains REVERT: C 282 LEU cc_start: 0.7679 (mt) cc_final: 0.7461 (mt) REVERT: C 292 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7652 (mtm180) outliers start: 33 outliers final: 30 residues processed: 204 average time/residue: 0.6093 time to fit residues: 135.4342 Evaluate side-chains 209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 188 LYS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 220 THR Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 306 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN J 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.188651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153185 restraints weight = 16021.305| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.27 r_work: 0.3557 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13862 Z= 0.146 Angle : 0.609 6.232 19665 Z= 0.336 Chirality : 0.042 0.214 2319 Planarity : 0.004 0.051 1697 Dihedral : 22.556 177.882 3784 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.63 % Allowed : 23.67 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1054 helix: 0.74 (0.22), residues: 557 sheet: 1.97 (0.54), residues: 87 loop : -1.22 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.012 0.001 TYR B 179 PHE 0.011 0.001 PHE A 92 TRP 0.005 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (13862) covalent geometry : angle 0.60857 / 0.34 (19665) hydrogen bonds : bond 0.05574 / 3.61 ( 607) hydrogen bonds : angle 3.99776 / 2.78 ( 1589) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: C 282 LEU cc_start: 0.7790 (mt) cc_final: 0.7590 (mt) REVERT: C 292 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7597 (mtm180) REVERT: B 31 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.8000 (mtm-85) REVERT: J 30 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6866 (pp) outliers start: 54 outliers final: 30 residues processed: 211 average time/residue: 0.6073 time to fit residues: 139.4675 Evaluate side-chains 205 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 82 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS B 76 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.188305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152205 restraints weight = 15945.899| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.28 r_work: 0.3555 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13862 Z= 0.152 Angle : 0.592 6.346 19665 Z= 0.325 Chirality : 0.042 0.253 2319 Planarity : 0.004 0.041 1697 Dihedral : 22.409 179.769 3752 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.80 % Allowed : 23.57 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1054 helix: 0.90 (0.22), residues: 564 sheet: 1.78 (0.54), residues: 90 loop : -1.21 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 31 TYR 0.014 0.001 TYR B 179 PHE 0.012 0.001 PHE B 96 TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (13862) covalent geometry : angle 0.59170 / 0.32 (19665) hydrogen bonds : bond 0.05238 / 3.40 ( 607) hydrogen bonds : angle 3.79680 / 2.64 ( 1589) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.335 Fit side-chains REVERT: C 292 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7569 (mtm180) REVERT: B 62 MET cc_start: 0.5242 (mpp) cc_final: 0.5013 (mpp) REVERT: B 251 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7166 (mm-30) REVERT: J 30 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6922 (pt) REVERT: J 91 VAL cc_start: 0.7292 (p) cc_final: 0.7090 (m) REVERT: J 298 ASN cc_start: 0.8622 (t0) cc_final: 0.8393 (t0) outliers start: 46 outliers final: 28 residues processed: 199 average time/residue: 0.5825 time to fit residues: 126.2469 Evaluate side-chains 199 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 149 LYS Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 295 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN B 104 ASN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151126 restraints weight = 15874.199| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.30 r_work: 0.3544 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13862 Z= 0.168 Angle : 0.603 7.202 19665 Z= 0.328 Chirality : 0.043 0.258 2319 Planarity : 0.004 0.041 1697 Dihedral : 22.370 179.927 3749 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.01 % Allowed : 23.67 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1054 helix: 0.99 (0.22), residues: 563 sheet: 1.71 (0.54), residues: 90 loop : -1.29 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.016 0.001 TYR B 179 PHE 0.014 0.002 PHE B 96 TRP 0.005 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13862) covalent geometry : angle 0.60336 / 0.33 (19665) hydrogen bonds : bond 0.05272 / 3.43 ( 607) hydrogen bonds : angle 3.73446 / 2.59 ( 1589) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.458 Fit side-chains REVERT: C 292 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7572 (mtm180) REVERT: B 62 MET cc_start: 0.5194 (mpp) cc_final: 0.4967 (mpp) REVERT: B 139 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 251 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7181 (mm-30) REVERT: J 30 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6925 (pt) REVERT: J 91 VAL cc_start: 0.7295 (p) cc_final: 0.7094 (m) REVERT: J 298 ASN cc_start: 0.8634 (t0) cc_final: 0.8386 (t0) outliers start: 48 outliers final: 35 residues processed: 207 average time/residue: 0.5425 time to fit residues: 122.4056 Evaluate side-chains 212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152694 restraints weight = 16009.825| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.30 r_work: 0.3552 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13862 Z= 0.142 Angle : 0.582 6.851 19665 Z= 0.316 Chirality : 0.042 0.234 2319 Planarity : 0.004 0.042 1697 Dihedral : 22.334 179.994 3744 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.90 % Allowed : 23.67 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1054 helix: 1.09 (0.22), residues: 568 sheet: 1.76 (0.54), residues: 90 loop : -1.25 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.015 0.001 TYR B 179 PHE 0.012 0.001 PHE B 96 TRP 0.004 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (13862) covalent geometry : angle 0.58222 / 0.32 (19665) hydrogen bonds : bond 0.04885 / 3.16 ( 607) hydrogen bonds : angle 3.66718 / 2.54 ( 1589) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.389 Fit side-chains REVERT: C 292 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7580 (mtm180) REVERT: B 62 MET cc_start: 0.5196 (mpp) cc_final: 0.4954 (mpp) REVERT: B 139 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7767 (mp) REVERT: J 30 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6913 (pt) REVERT: J 91 VAL cc_start: 0.7315 (p) cc_final: 0.7100 (m) REVERT: J 298 ASN cc_start: 0.8630 (t0) cc_final: 0.8396 (t0) outliers start: 47 outliers final: 33 residues processed: 201 average time/residue: 0.5798 time to fit residues: 127.1651 Evaluate side-chains 209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 145 LYS Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 0.0020 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144207 restraints weight = 15879.019| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.25 r_work: 0.3553 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13862 Z= 0.153 Angle : 0.587 6.982 19665 Z= 0.318 Chirality : 0.042 0.247 2319 Planarity : 0.004 0.041 1697 Dihedral : 22.288 179.609 3741 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.90 % Allowed : 23.67 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1054 helix: 1.17 (0.22), residues: 566 sheet: 1.82 (0.54), residues: 90 loop : -1.26 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.016 0.001 TYR B 179 PHE 0.013 0.001 PHE B 96 TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (13862) covalent geometry : angle 0.58737 / 0.32 (19665) hydrogen bonds : bond 0.04946 / 3.21 ( 607) hydrogen bonds : angle 3.62222 / 2.51 ( 1589) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.394 Fit side-chains REVERT: C 292 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7568 (mtm180) REVERT: B 62 MET cc_start: 0.5168 (mpp) cc_final: 0.4923 (mpp) REVERT: B 139 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 251 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7157 (mm-30) REVERT: J 30 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6881 (pt) REVERT: J 91 VAL cc_start: 0.7294 (p) cc_final: 0.7072 (m) REVERT: J 298 ASN cc_start: 0.8638 (t0) cc_final: 0.8399 (t0) outliers start: 47 outliers final: 35 residues processed: 206 average time/residue: 0.5931 time to fit residues: 133.1723 Evaluate side-chains 214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 261 GLN B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143794 restraints weight = 15965.908| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.24 r_work: 0.3546 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13862 Z= 0.173 Angle : 0.603 7.128 19665 Z= 0.325 Chirality : 0.043 0.258 2319 Planarity : 0.004 0.041 1697 Dihedral : 22.278 179.735 3738 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.80 % Allowed : 24.09 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1054 helix: 1.13 (0.22), residues: 566 sheet: 1.82 (0.54), residues: 90 loop : -1.29 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.017 0.001 TYR B 179 PHE 0.014 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (13862) covalent geometry : angle 0.60306 / 0.33 (19665) hydrogen bonds : bond 0.05183 / 3.37 ( 607) hydrogen bonds : angle 3.63328 / 2.52 ( 1589) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.408 Fit side-chains REVERT: B 62 MET cc_start: 0.5229 (mpp) cc_final: 0.4986 (mpp) REVERT: B 139 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7791 (mp) REVERT: B 251 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7142 (mm-30) REVERT: J 30 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6746 (pp) REVERT: J 91 VAL cc_start: 0.7281 (p) cc_final: 0.7055 (m) REVERT: J 93 VAL cc_start: 0.3263 (OUTLIER) cc_final: 0.2819 (m) REVERT: J 298 ASN cc_start: 0.8632 (t0) cc_final: 0.8392 (t0) outliers start: 46 outliers final: 36 residues processed: 211 average time/residue: 0.5960 time to fit residues: 137.1356 Evaluate side-chains 216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.188238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151970 restraints weight = 15773.935| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.30 r_work: 0.3540 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13862 Z= 0.163 Angle : 0.596 7.076 19665 Z= 0.321 Chirality : 0.042 0.253 2319 Planarity : 0.004 0.046 1697 Dihedral : 22.272 179.914 3738 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.59 % Allowed : 24.50 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 1054 helix: 1.17 (0.22), residues: 566 sheet: 1.84 (0.53), residues: 90 loop : -1.30 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.016 0.001 TYR B 179 PHE 0.013 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (13862) covalent geometry : angle 0.59568 / 0.32 (19665) hydrogen bonds : bond 0.05044 / 3.28 ( 607) hydrogen bonds : angle 3.60712 / 2.50 ( 1589) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.415 Fit side-chains REVERT: C 292 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7467 (mtm180) REVERT: B 62 MET cc_start: 0.5219 (mpp) cc_final: 0.4968 (mpp) REVERT: B 139 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 251 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7165 (mm-30) REVERT: J 30 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6875 (pt) REVERT: J 93 VAL cc_start: 0.3272 (OUTLIER) cc_final: 0.2662 (m) REVERT: J 298 ASN cc_start: 0.8634 (t0) cc_final: 0.8395 (t0) outliers start: 44 outliers final: 34 residues processed: 207 average time/residue: 0.5992 time to fit residues: 135.3723 Evaluate side-chains 214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.143688 restraints weight = 16095.675| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.22 r_work: 0.3547 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13862 Z= 0.159 Angle : 0.591 7.070 19665 Z= 0.319 Chirality : 0.042 0.250 2319 Planarity : 0.004 0.048 1697 Dihedral : 22.257 179.931 3736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.69 % Allowed : 24.61 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1054 helix: 1.19 (0.22), residues: 566 sheet: 1.90 (0.53), residues: 90 loop : -1.28 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.016 0.001 TYR B 179 PHE 0.013 0.002 PHE B 96 TRP 0.005 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (13862) covalent geometry : angle 0.59124 / 0.32 (19665) hydrogen bonds : bond 0.04958 / 3.23 ( 607) hydrogen bonds : angle 3.58709 / 2.48 ( 1589) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.446 Fit side-chains REVERT: C 292 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7544 (mtm180) REVERT: B 62 MET cc_start: 0.5166 (mpp) cc_final: 0.4924 (mpp) REVERT: B 139 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 251 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7133 (mm-30) REVERT: J 30 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6818 (pt) REVERT: J 298 ASN cc_start: 0.8641 (t0) cc_final: 0.8403 (t0) outliers start: 45 outliers final: 38 residues processed: 203 average time/residue: 0.6085 time to fit residues: 134.6562 Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 229 ILE Chi-restraints excluded: chain J residue 230 LYS Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 105 optimal weight: 5.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144173 restraints weight = 16115.355| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.22 r_work: 0.3553 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13862 Z= 0.136 Angle : 0.582 6.946 19665 Z= 0.314 Chirality : 0.041 0.244 2319 Planarity : 0.004 0.053 1697 Dihedral : 22.247 179.932 3736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.38 % Allowed : 25.03 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1054 helix: 1.25 (0.22), residues: 566 sheet: 1.92 (0.53), residues: 90 loop : -1.28 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.017 0.001 TYR B 179 PHE 0.012 0.001 PHE B 96 TRP 0.004 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (13862) covalent geometry : angle 0.58243 / 0.31 (19665) hydrogen bonds : bond 0.04776 / 3.11 ( 607) hydrogen bonds : angle 3.57328 / 2.47 ( 1589) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.389 Fit side-chains REVERT: C 292 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7540 (mtm180) REVERT: B 62 MET cc_start: 0.5174 (mpp) cc_final: 0.4923 (mpp) REVERT: B 139 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7752 (mp) REVERT: B 251 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7130 (mm-30) REVERT: J 30 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6703 (pp) REVERT: J 93 VAL cc_start: 0.3206 (OUTLIER) cc_final: 0.2633 (m) REVERT: J 298 ASN cc_start: 0.8632 (t0) cc_final: 0.8393 (t0) outliers start: 42 outliers final: 34 residues processed: 207 average time/residue: 0.6009 time to fit residues: 135.4602 Evaluate side-chains 218 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 184 LYS Chi-restraints excluded: chain J residue 189 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain J residue 196 ILE Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 261 GLN Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain J residue 273 VAL Chi-restraints excluded: chain J residue 277 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN J 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143328 restraints weight = 15961.798| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.23 r_work: 0.3546 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13862 Z= 0.168 Angle : 0.600 7.124 19665 Z= 0.323 Chirality : 0.043 0.257 2319 Planarity : 0.004 0.050 1697 Dihedral : 22.248 179.808 3736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.96 % Allowed : 25.55 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1054 helix: 1.19 (0.22), residues: 566 sheet: 1.97 (0.54), residues: 89 loop : -1.28 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 49 TYR 0.016 0.001 TYR B 179 PHE 0.014 0.002 PHE B 96 TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (13862) covalent geometry : angle 0.60020 / 0.32 (19665) hydrogen bonds : bond 0.05065 / 3.30 ( 607) hydrogen bonds : angle 3.59483 / 2.49 ( 1589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6073.86 seconds wall clock time: 104 minutes 0.89 seconds (6240.89 seconds total)