Starting phenix.real_space_refine on Thu Jul 31 06:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_33226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_33226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_33226.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_33226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjg_33226/07_2025/7xjg_33226.cif" } resolution = 2.51 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.32, per 1000 atoms: 0.63 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: 3.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.67 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: 4.16 Time building geometry restraints manager: 3.63 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=" N ARG B 213 " pdb=" CA ARG B 213 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.28e+00 bond pdb=" N ILE A 41 " pdb=" CA ILE A 41 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.22e+00 bond pdb=" N VAL B 210 " pdb=" CA VAL B 210 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.77e+00 bond pdb=" N ARG A 47 " pdb=" CA ARG A 47 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.66e+00 ... (remaining 13857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 19163 2.06 - 4.13: 437 4.13 - 6.19: 57 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=" 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=" C4' DC G 3 " pdb=" C3' DC G 3 " pdb=" O3' DC G 3 " ideal model delta sigma weight residual 110.00 116.83 -6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" CB LYS J 184 " pdb=" CG LYS J 184 " pdb=" CD LYS J 184 " ideal model delta sigma weight residual 111.30 121.22 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" C LYS B 211 " pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 110.38 119.11 -8.73 2.04e+00 2.40e-01 1.83e+01 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7552 35.95 - 71.89: 820 71.89 - 107.84: 39 107.84 - 143.78: 8 143.78 - 179.73: 15 Dihedral angle restraints: 8434 sinusoidal: 5307 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 8431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1927 0.056 - 0.111: 305 0.111 - 0.167: 70 0.167 - 0.222: 16 0.222 - 0.278: 1 Chirality restraints: 2319 Sorted by residual: 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 chirality pdb=" P G I 1 " pdb=" OP1 G I 1 " pdb=" OP2 G I 1 " pdb=" O5' G I 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.63 -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: 3.740 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.280 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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= 0.255 Angle : 0.712 10.322 19665 Z= 0.419 Chirality : 0.046 0.278 2319 Planarity : 0.005 0.060 1697 Dihedral : 24.504 179.725 6414 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 (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: -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 TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.015 0.002 PHE B 96 TYR 0.024 0.002 TYR B 184 ARG 0.008 0.001 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.16129 ( 607) hydrogen bonds : angle 5.30362 ( 1589) covalent geometry : bond 0.00486 (13862) covalent geometry : angle 0.71244 (19665) *********************** 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 : 1.074 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: 1.4935 time to fit residues: 331.1432 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 : 1.127 ------------------------------------------------------------------------------- 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 103 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 104 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.186881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150598 restraints weight = 15818.764| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.33 r_work: 0.3524 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13862 Z= 0.204 Angle : 0.622 7.523 19665 Z= 0.334 Chirality : 0.041 0.186 2319 Planarity : 0.005 0.048 1697 Dihedral : 25.386 178.371 4292 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.74 % Allowed : 22.94 % 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 (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: -0.04 (0.25), residues: 1054 helix: 0.58 (0.22), residues: 566 sheet: 1.66 (0.53), residues: 89 loop : -1.28 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.016 0.002 PHE B 96 TYR 0.017 0.002 TYR B 179 ARG 0.005 0.001 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.05642 ( 607) hydrogen bonds : angle 3.94330 ( 1589) covalent geometry : bond 0.00462 (13862) covalent geometry : angle 0.62247 (19665) *********************** 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 231 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.898 Fit side-chains REVERT: A 63 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6868 (ttm-80) REVERT: C 292 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7622 (mtm180) REVERT: J 30 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6950 (pt) REVERT: J 86 ILE cc_start: 0.7681 (tt) cc_final: 0.7220 (pt) REVERT: J 91 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6968 (p) outliers start: 55 outliers final: 27 residues processed: 210 average time/residue: 1.6541 time to fit residues: 379.5245 Evaluate side-chains 204 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG 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 247 VAL Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 193 THR 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 53 LEU Chi-restraints excluded: chain J residue 91 VAL 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 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 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 2 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 0.0040 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.188429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152594 restraints weight = 15994.711| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.27 r_work: 0.3564 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13862 Z= 0.143 Angle : 0.555 6.860 19665 Z= 0.297 Chirality : 0.038 0.173 2319 Planarity : 0.004 0.045 1697 Dihedral : 25.121 179.930 4257 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.69 % Allowed : 23.46 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.26), residues: 1054 helix: 1.01 (0.22), residues: 565 sheet: 1.70 (0.53), residues: 90 loop : -1.14 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 PHE 0.011 0.001 PHE B 96 TYR 0.014 0.001 TYR B 179 ARG 0.005 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 607) hydrogen bonds : angle 3.61937 ( 1589) covalent geometry : bond 0.00313 (13862) covalent geometry : angle 0.55519 (19665) *********************** 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 222 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.073 Fit side-chains REVERT: C 251 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7362 (mpt180) REVERT: B 62 MET cc_start: 0.5199 (mpp) cc_final: 0.4964 (mpp) REVERT: B 139 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (mp) REVERT: B 158 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8340 (pp) REVERT: B 251 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7118 (mm-30) REVERT: J 30 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6870 (pt) REVERT: J 60 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6753 (t70) REVERT: J 87 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7485 (tm) REVERT: J 91 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6961 (p) REVERT: J 180 MET cc_start: 0.5198 (mmm) cc_final: 0.4979 (mmm) REVERT: J 298 ASN cc_start: 0.8590 (t0) cc_final: 0.8370 (t0) outliers start: 45 outliers final: 24 residues processed: 205 average time/residue: 1.3003 time to fit residues: 289.7693 Evaluate side-chains 204 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain C residue 14 ILE 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 158 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 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 115 ASN 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 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 239 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN ** 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 = 0.4181 r_free = 0.4181 target = 0.177999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142424 restraints weight = 15875.178| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.23 r_work: 0.3529 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13862 Z= 0.203 Angle : 0.605 7.300 19665 Z= 0.323 Chirality : 0.041 0.179 2319 Planarity : 0.005 0.046 1697 Dihedral : 25.127 179.422 4246 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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 (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: 0.29 (0.25), residues: 1054 helix: 0.96 (0.22), residues: 567 sheet: 1.63 (0.53), residues: 90 loop : -1.28 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.007 0.001 HIS B 280 PHE 0.015 0.002 PHE B 96 TYR 0.018 0.002 TYR A 179 ARG 0.005 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05432 ( 607) hydrogen bonds : angle 3.71487 ( 1589) covalent geometry : bond 0.00465 (13862) covalent geometry : angle 0.60538 (19665) *********************** 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 229 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.249 Fit side-chains REVERT: B 62 MET cc_start: 0.5158 (mpp) cc_final: 0.4927 (mpp) REVERT: B 139 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7732 (mp) REVERT: J 30 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6758 (pp) REVERT: J 60 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6736 (t70) REVERT: J 91 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6954 (p) REVERT: J 180 MET cc_start: 0.5266 (mmm) cc_final: 0.5053 (mmm) REVERT: J 298 ASN cc_start: 0.8625 (t0) cc_final: 0.8395 (t0) outliers start: 47 outliers final: 31 residues processed: 211 average time/residue: 1.2435 time to fit residues: 285.7968 Evaluate side-chains 210 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 177 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 60 ASP Chi-restraints excluded: chain J residue 91 VAL 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 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 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 68 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143301 restraints weight = 16063.502| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.22 r_work: 0.3542 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13862 Z= 0.160 Angle : 0.580 8.112 19665 Z= 0.309 Chirality : 0.039 0.175 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.100 179.510 4246 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.80 % Allowed : 23.36 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.25), residues: 1054 helix: 1.09 (0.22), residues: 567 sheet: 1.69 (0.53), residues: 90 loop : -1.29 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.013 0.001 PHE B 96 TYR 0.015 0.001 TYR B 179 ARG 0.005 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 607) hydrogen bonds : angle 3.64277 ( 1589) covalent geometry : bond 0.00355 (13862) covalent geometry : angle 0.57975 (19665) *********************** 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 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.173 Fit side-chains REVERT: B 62 MET cc_start: 0.5175 (mpp) cc_final: 0.4925 (mpp) REVERT: B 139 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7735 (mp) REVERT: J 30 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6872 (pt) REVERT: J 91 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6985 (p) REVERT: J 180 MET cc_start: 0.5282 (mmm) cc_final: 0.5057 (mmm) REVERT: J 298 ASN cc_start: 0.8613 (t0) cc_final: 0.8388 (t0) outliers start: 46 outliers final: 34 residues processed: 204 average time/residue: 1.2631 time to fit residues: 280.7590 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 : 1.054 ------------------------------------------------------------------------------- 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 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 23 LEU 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 49 LEU Chi-restraints excluded: chain J residue 91 VAL 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 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 257 THR 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 112 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 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 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 = 0.179053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143393 restraints weight = 16183.084| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.23 r_work: 0.3542 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13862 Z= 0.162 Angle : 0.576 7.578 19665 Z= 0.306 Chirality : 0.039 0.174 2319 Planarity : 0.004 0.048 1697 Dihedral : 25.073 179.444 4246 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.48 % Allowed : 23.36 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.26), residues: 1054 helix: 1.15 (0.22), residues: 567 sheet: 1.69 (0.53), residues: 90 loop : -1.28 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.013 0.001 PHE B 96 TYR 0.015 0.001 TYR B 179 ARG 0.007 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 607) hydrogen bonds : angle 3.60364 ( 1589) covalent geometry : bond 0.00362 (13862) covalent geometry : angle 0.57567 (19665) *********************** 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 220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.191 Fit side-chains REVERT: B 62 MET cc_start: 0.5151 (mpp) cc_final: 0.4914 (mpp) REVERT: B 139 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 251 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7121 (mm-30) REVERT: J 30 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6860 (pt) REVERT: J 91 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6948 (p) REVERT: J 180 MET cc_start: 0.5333 (mmm) cc_final: 0.5084 (mmm) REVERT: J 298 ASN cc_start: 0.8621 (t0) cc_final: 0.8387 (t0) outliers start: 43 outliers final: 34 residues processed: 206 average time/residue: 1.2591 time to fit residues: 283.0954 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 : 1.055 ------------------------------------------------------------------------------- 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 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 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 91 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER 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 257 THR 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 81 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.179359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143812 restraints weight = 16078.545| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.23 r_work: 0.3548 rms_B_bonded: 2.46 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: 0.7633 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13862 Z= 0.153 Angle : 0.567 7.565 19665 Z= 0.302 Chirality : 0.038 0.173 2319 Planarity : 0.004 0.047 1697 Dihedral : 25.045 179.316 4246 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.59 % Allowed : 23.98 % 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 (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: 0.54 (0.26), residues: 1054 helix: 1.22 (0.22), residues: 567 sheet: 1.78 (0.53), residues: 90 loop : -1.26 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.012 0.001 PHE B 96 TYR 0.015 0.001 TYR B 179 ARG 0.006 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 607) hydrogen bonds : angle 3.56478 ( 1589) covalent geometry : bond 0.00341 (13862) covalent geometry : angle 0.56657 (19665) *********************** 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 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.025 Fit side-chains REVERT: C 251 ARG cc_start: 0.7704 (mmt180) cc_final: 0.7407 (mpt180) REVERT: B 62 MET cc_start: 0.5173 (mpp) cc_final: 0.4921 (mpp) REVERT: B 139 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7730 (mp) REVERT: J 30 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6859 (pt) REVERT: J 91 VAL cc_start: 0.7162 (OUTLIER) cc_final: 0.6935 (p) REVERT: J 180 MET cc_start: 0.5358 (mmm) cc_final: 0.5093 (mmm) REVERT: J 298 ASN cc_start: 0.8609 (t0) cc_final: 0.8372 (t0) outliers start: 44 outliers final: 34 residues processed: 210 average time/residue: 1.2490 time to fit residues: 285.2940 Evaluate side-chains 215 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 23 LEU 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 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 91 VAL 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 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 257 THR 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 17 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 24 optimal weight: 0.0020 chunk 82 optimal weight: 2.9990 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN B 240 GLN ** 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 = 0.4197 r_free = 0.4197 target = 0.179400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143794 restraints weight = 16170.198| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.24 r_work: 0.3551 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13862 Z= 0.153 Angle : 0.565 7.258 19665 Z= 0.301 Chirality : 0.038 0.173 2319 Planarity : 0.004 0.046 1697 Dihedral : 25.013 179.107 4244 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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 (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: 0.59 (0.26), residues: 1054 helix: 1.27 (0.22), residues: 566 sheet: 1.82 (0.53), residues: 90 loop : -1.25 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.012 0.001 PHE B 96 TYR 0.015 0.001 TYR B 179 ARG 0.007 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 607) hydrogen bonds : angle 3.53851 ( 1589) covalent geometry : bond 0.00341 (13862) covalent geometry : angle 0.56501 (19665) *********************** 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 223 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 1.305 Fit side-chains REVERT: B 31 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: B 62 MET cc_start: 0.5156 (mpp) cc_final: 0.4921 (mpp) REVERT: B 139 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (mp) REVERT: J 30 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6858 (pt) REVERT: J 91 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6989 (p) REVERT: J 180 MET cc_start: 0.5363 (mmm) cc_final: 0.5078 (mmm) REVERT: J 298 ASN cc_start: 0.8616 (t0) cc_final: 0.8377 (t0) outliers start: 46 outliers final: 38 residues processed: 207 average time/residue: 1.2999 time to fit residues: 293.0486 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 : 1.057 ------------------------------------------------------------------------------- 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 239 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 31 ARG 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 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 49 LEU Chi-restraints excluded: chain J residue 91 VAL 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 234 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 257 THR 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 67 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 92 optimal weight: 0.0010 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.180071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144492 restraints weight = 16007.848| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.24 r_work: 0.3559 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13862 Z= 0.130 Angle : 0.556 7.087 19665 Z= 0.296 Chirality : 0.037 0.172 2319 Planarity : 0.004 0.056 1697 Dihedral : 25.000 179.063 4244 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.48 % Allowed : 24.30 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.26), residues: 1054 helix: 1.32 (0.22), residues: 568 sheet: 1.88 (0.53), residues: 90 loop : -1.23 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 PHE 0.012 0.001 PHE J 205 TYR 0.015 0.001 TYR B 179 ARG 0.006 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 607) hydrogen bonds : angle 3.50214 ( 1589) covalent geometry : bond 0.00285 (13862) covalent geometry : angle 0.55565 (19665) *********************** 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 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.139 Fit side-chains REVERT: C 292 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7564 (mtm180) REVERT: B 62 MET cc_start: 0.5166 (mpp) cc_final: 0.4925 (mpp) REVERT: B 139 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7720 (mp) REVERT: J 30 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6857 (pt) REVERT: J 91 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6974 (p) REVERT: J 180 MET cc_start: 0.5362 (mmm) cc_final: 0.5077 (mmm) REVERT: J 298 ASN cc_start: 0.8608 (t0) cc_final: 0.8369 (t0) outliers start: 43 outliers final: 36 residues processed: 205 average time/residue: 1.4545 time to fit residues: 325.8784 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 : 1.702 ------------------------------------------------------------------------------- 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 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 23 LEU 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 20 LYS Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER 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 239 ILE Chi-restraints excluded: chain J residue 257 THR 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 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 113 optimal weight: 0.0370 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4185 r_free = 0.4185 target = 0.178313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142448 restraints weight = 15917.282| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.25 r_work: 0.3531 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13862 Z= 0.192 Angle : 0.600 7.239 19665 Z= 0.318 Chirality : 0.040 0.177 2319 Planarity : 0.004 0.049 1697 Dihedral : 25.014 179.111 4244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.28 % Allowed : 24.19 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.26), residues: 1054 helix: 1.16 (0.22), residues: 569 sheet: 1.84 (0.53), residues: 90 loop : -1.33 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.014 0.002 PHE B 96 TYR 0.017 0.002 TYR A 179 ARG 0.010 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.05220 ( 607) hydrogen bonds : angle 3.58865 ( 1589) covalent geometry : bond 0.00438 (13862) covalent geometry : angle 0.60006 (19665) ********************** 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 219 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 1.226 Fit side-chains REVERT: A 11 ARG cc_start: 0.7998 (tpt-90) cc_final: 0.7750 (mtp85) REVERT: C 279 LEU cc_start: 0.7112 (mt) cc_final: 0.6875 (mt) REVERT: B 31 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (mtm-85) REVERT: B 62 MET cc_start: 0.5143 (mpp) cc_final: 0.4906 (mpp) REVERT: B 139 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7774 (mp) REVERT: J 30 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6844 (pt) REVERT: J 91 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.7005 (p) REVERT: J 180 MET cc_start: 0.5345 (mmm) cc_final: 0.5057 (mmm) REVERT: J 298 ASN cc_start: 0.8657 (t0) cc_final: 0.8413 (t0) outliers start: 41 outliers final: 34 residues processed: 206 average time/residue: 1.3402 time to fit residues: 300.3992 Evaluate side-chains 217 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 31 ARG 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 49 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 155 SER 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 239 ILE Chi-restraints excluded: chain J residue 257 THR 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 77 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4191 r_free = 0.4191 target = 0.178844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143075 restraints weight = 16148.647| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.24 r_work: 0.3539 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1283 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= 0.159 Angle : 0.585 7.035 19665 Z= 0.310 Chirality : 0.039 0.173 2319 Planarity : 0.004 0.050 1697 Dihedral : 25.005 179.122 4244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.48 % Allowed : 24.19 % 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 (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: 0.50 (0.25), residues: 1054 helix: 1.20 (0.22), residues: 569 sheet: 1.86 (0.53), residues: 90 loop : -1.34 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 PHE 0.013 0.001 PHE B 96 TYR 0.017 0.001 TYR A 179 ARG 0.009 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 607) hydrogen bonds : angle 3.56244 ( 1589) covalent geometry : bond 0.00354 (13862) covalent geometry : angle 0.58519 (19665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13757.60 seconds wall clock time: 243 minutes 19.90 seconds (14599.90 seconds total)