Starting phenix.real_space_refine on Thu Sep 18 00:18:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp2_45797/09_2025/9cp2_45797.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 406 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 36 5.16 5 C 7435 2.51 5 N 1963 2.21 5 O 2342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11813 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1926 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain breaks: 4 Chain: "A" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2458 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "G" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1688 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Chain: "S" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 572 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "M" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 221 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'TRS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.87, per 1000 atoms: 0.24 Number of scatterers: 11813 At special positions: 0 Unit cell: (82.36, 102.24, 151.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 37 15.00 O 2342 8.00 N 1963 7.00 C 7435 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: 0.98 Conformation dependent library (CDL) restraints added in 401.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 20 sheets defined 33.8% alpha, 16.6% beta 8 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 50 through 69 removed outlier: 4.004A pdb=" N ALA B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.879A pdb=" N GLN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.588A pdb=" N LEU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.575A pdb=" N ASP B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.805A pdb=" N LEU B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.945A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.858A pdb=" N GLY B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 4.020A pdb=" N LEU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.801A pdb=" N ALA C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.796A pdb=" N GLN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.534A pdb=" N LEU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 4.298A pdb=" N ARG C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.639A pdb=" N LEU C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.831A pdb=" N LEU C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.755A pdb=" N THR C 273 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.995A pdb=" N LEU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.980A pdb=" N GLN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 100 through 113 removed outlier: 4.335A pdb=" N ARG D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG D 106 " --> pdb=" O ASN D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.532A pdb=" N LEU D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 4.505A pdb=" N LEU D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.806A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 279 " --> pdb=" O MET D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'A' and resid 50 through 69 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.903A pdb=" N GLN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 207 through 225 removed outlier: 4.845A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 4.120A pdb=" N LEU A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.731A pdb=" N THR A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.802A pdb=" N LEU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 removed outlier: 3.583A pdb=" N LEU G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 138 Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.951A pdb=" N ILE G 198 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 8 current: chain 'B' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 190 current: chain 'B' and resid 289 through 295 removed outlier: 3.809A pdb=" N THR B 306 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 10 through 13 current: chain 'B' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 27 current: chain 'B' and resid 174 through 182 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 8 current: chain 'C' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 190 current: chain 'C' and resid 289 through 295 removed outlier: 3.778A pdb=" N THR C 306 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 27 current: chain 'C' and resid 174 through 182 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 35 Processing sheet with id=AA8, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AA9, first strand: chain 'D' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 2 through 8 current: chain 'D' and resid 184 through 190 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 190 current: chain 'D' and resid 289 through 295 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 29 through 36 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AB3, first strand: chain 'A' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 13 current: chain 'A' and resid 174 through 182 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 182 current: chain 'A' and resid 290 through 295 Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB5, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 73 removed outlier: 6.909A pdb=" N TYR G 3 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL G 157 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS G 5 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL G 155 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE G 7 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.558A pdb=" N PHE G 14 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 161 through 163 removed outlier: 7.472A pdb=" N GLU G 228 " --> pdb=" O PHE G 239 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AC1, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AC2, first strand: chain 'G' and resid 212 through 213 removed outlier: 3.559A pdb=" N ALA G 218 " --> pdb=" O THR G 213 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3210 1.33 - 1.45: 2030 1.45 - 1.57: 6712 1.57 - 1.69: 73 1.69 - 1.81: 69 Bond restraints: 12094 Sorted by residual: bond pdb=" N TRS B 401 " pdb=" C TRS B 401 " ideal model delta sigma weight residual 1.501 1.463 0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" N TRS C 401 " pdb=" C TRS C 401 " ideal model delta sigma weight residual 1.501 1.463 0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" N TRS S 402 " pdb=" C TRS S 402 " ideal model delta sigma weight residual 1.501 1.464 0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" N TRS S 401 " pdb=" C TRS S 401 " ideal model delta sigma weight residual 1.501 1.465 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" CG LEU A 12 " pdb=" CD2 LEU A 12 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.80e-01 ... (remaining 12089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 15802 1.08 - 2.17: 530 2.17 - 3.25: 131 3.25 - 4.33: 21 4.33 - 5.41: 7 Bond angle restraints: 16491 Sorted by residual: angle pdb=" N GLU A 13 " pdb=" CA GLU A 13 " pdb=" C GLU A 13 " ideal model delta sigma weight residual 109.40 112.73 -3.33 1.63e+00 3.76e-01 4.16e+00 angle pdb=" N GLU C 13 " pdb=" CA GLU C 13 " pdb=" C GLU C 13 " ideal model delta sigma weight residual 109.24 112.63 -3.39 1.67e+00 3.59e-01 4.11e+00 angle pdb=" N THR G 141 " pdb=" CA THR G 141 " pdb=" C THR G 141 " ideal model delta sigma weight residual 110.80 115.09 -4.29 2.13e+00 2.20e-01 4.06e+00 angle pdb=" C THR G 141 " pdb=" N ARG G 142 " pdb=" CA ARG G 142 " ideal model delta sigma weight residual 121.94 118.67 3.27 1.76e+00 3.23e-01 3.45e+00 angle pdb=" N ALA C 30 " pdb=" CA ALA C 30 " pdb=" C ALA C 30 " ideal model delta sigma weight residual 108.25 110.38 -2.13 1.16e+00 7.43e-01 3.36e+00 ... (remaining 16486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.28: 7007 29.28 - 58.56: 274 58.56 - 87.84: 33 87.84 - 117.13: 2 117.13 - 146.41: 1 Dihedral angle restraints: 7317 sinusoidal: 3264 harmonic: 4053 Sorted by residual: dihedral pdb=" O4' U S 2 " pdb=" C1' U S 2 " pdb=" N1 U S 2 " pdb=" C2 U S 2 " ideal model delta sinusoidal sigma weight residual -128.00 -23.46 -104.54 1 1.70e+01 3.46e-03 4.16e+01 dihedral pdb=" CA LEU C 12 " pdb=" C LEU C 12 " pdb=" N GLU C 13 " pdb=" CA GLU C 13 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" O4' U S 15 " pdb=" C1' U S 15 " pdb=" N1 U S 15 " pdb=" C2 U S 15 " ideal model delta sinusoidal sigma weight residual -128.00 -66.12 -61.88 1 1.70e+01 3.46e-03 1.76e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1350 0.038 - 0.077: 385 0.077 - 0.115: 131 0.115 - 0.153: 35 0.153 - 0.192: 2 Chirality restraints: 1903 Sorted by residual: chirality pdb=" CB VAL B 18 " pdb=" CA VAL B 18 " pdb=" CG1 VAL B 18 " pdb=" CG2 VAL B 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CB ILE G 114 " pdb=" CA ILE G 114 " pdb=" CG1 ILE G 114 " pdb=" CG2 ILE G 114 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB VAL C 18 " pdb=" CA VAL C 18 " pdb=" CG1 VAL C 18 " pdb=" CG2 VAL C 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1900 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 30 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 31 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 108 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLU C 108 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU C 108 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 109 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 108 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLU B 108 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU B 108 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 109 " -0.009 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 111 2.65 - 3.21: 10044 3.21 - 3.78: 16730 3.78 - 4.34: 23295 4.34 - 4.90: 39516 Nonbonded interactions: 89696 Sorted by model distance: nonbonded pdb=" O PHE B 159 " pdb=" NH2 ARG C 28 " model vdw 2.089 3.120 nonbonded pdb=" NH2 ARG B 28 " pdb=" O PHE A 159 " model vdw 2.193 3.120 nonbonded pdb=" OE1 GLU D 108 " pdb=" OG1 THR D 200 " model vdw 2.217 3.040 nonbonded pdb=" O THR A 134 " pdb=" NH1 ARG A 136 " model vdw 2.266 3.120 nonbonded pdb=" ND1 HIS C 55 " pdb=" OP2 A S 20 " model vdw 2.311 3.120 ... (remaining 89691 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' and resid 1 through 321) selection = (chain 'C' and resid 1 through 321) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.003 0.038 12094 Z= 0.133 Angle : 0.504 5.414 16491 Z= 0.274 Chirality : 0.043 0.192 1903 Planarity : 0.004 0.043 1956 Dihedral : 15.145 146.408 4719 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1381 helix: 0.55 (0.25), residues: 442 sheet: 0.70 (0.27), residues: 306 loop : -1.17 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 46 TYR 0.015 0.001 TYR G 208 PHE 0.020 0.001 PHE B 159 TRP 0.010 0.001 TRP G 12 HIS 0.003 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00285 (12094) covalent geometry : angle 0.50441 (16491) hydrogen bonds : bond 0.15178 ( 374) hydrogen bonds : angle 5.92528 ( 1028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 TYR cc_start: 0.7248 (m-80) cc_final: 0.6977 (m-10) REVERT: C 233 ASN cc_start: 0.7692 (m-40) cc_final: 0.7233 (t0) REVERT: C 276 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7062 (mtm-85) REVERT: C 287 ASN cc_start: 0.8737 (t0) cc_final: 0.8443 (t0) REVERT: D 1 MET cc_start: 0.7640 (mtp) cc_final: 0.7429 (mtp) REVERT: D 78 GLN cc_start: 0.9123 (mp10) cc_final: 0.8891 (mp10) REVERT: D 193 ASP cc_start: 0.8832 (m-30) cc_final: 0.8600 (p0) REVERT: D 248 MET cc_start: 0.6266 (mmm) cc_final: 0.5440 (mmt) REVERT: D 260 MET cc_start: 0.8293 (mtm) cc_final: 0.8023 (ptp) REVERT: D 276 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7083 (ttm170) REVERT: A 96 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8647 (mtpp) REVERT: G 118 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7195 (mtt90) REVERT: G 209 ILE cc_start: 0.8308 (mt) cc_final: 0.7991 (mp) outliers start: 3 outliers final: 2 residues processed: 197 average time/residue: 0.6559 time to fit residues: 138.5091 Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain A residue 201 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 160 HIS C 11 ASN C 160 HIS C 265 HIS A 160 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081334 restraints weight = 24854.846| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.26 r_work: 0.3168 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 12094 Z= 0.341 Angle : 0.732 12.417 16491 Z= 0.381 Chirality : 0.048 0.162 1903 Planarity : 0.005 0.050 1956 Dihedral : 14.441 150.978 2055 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.09 % Allowed : 9.28 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.21), residues: 1381 helix: 0.43 (0.24), residues: 442 sheet: -0.01 (0.28), residues: 304 loop : -1.54 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 136 TYR 0.020 0.002 TYR G 172 PHE 0.021 0.002 PHE A 159 TRP 0.016 0.002 TRP G 138 HIS 0.010 0.003 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00800 (12094) covalent geometry : angle 0.73171 (16491) hydrogen bonds : bond 0.06442 ( 374) hydrogen bonds : angle 4.76696 ( 1028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9154 (mtm) cc_final: 0.7950 (ttm) REVERT: B 13 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8209 (pp20) REVERT: B 204 LYS cc_start: 0.7887 (tptt) cc_final: 0.7619 (tptt) REVERT: C 101 TYR cc_start: 0.7523 (m-80) cc_final: 0.6988 (m-10) REVERT: C 233 ASN cc_start: 0.8329 (m-40) cc_final: 0.7424 (t0) REVERT: C 287 ASN cc_start: 0.8901 (t0) cc_final: 0.8608 (t0) REVERT: D 248 MET cc_start: 0.5971 (mmm) cc_final: 0.5468 (mmt) REVERT: D 260 MET cc_start: 0.8422 (mtm) cc_final: 0.8053 (ptp) REVERT: D 276 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.6753 (ttm110) REVERT: A 96 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8726 (mtpp) REVERT: A 101 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.8084 (p90) REVERT: A 124 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8431 (ttt) REVERT: A 201 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7741 (t80) REVERT: G 118 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7491 (mtt90) REVERT: G 180 VAL cc_start: 0.8397 (p) cc_final: 0.7990 (m) REVERT: G 209 ILE cc_start: 0.7597 (mt) cc_final: 0.7349 (mp) outliers start: 37 outliers final: 12 residues processed: 115 average time/residue: 0.5669 time to fit residues: 70.8936 Evaluate side-chains 91 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084693 restraints weight = 24820.265| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.31 r_work: 0.3229 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12094 Z= 0.132 Angle : 0.521 7.073 16491 Z= 0.274 Chirality : 0.042 0.146 1903 Planarity : 0.004 0.041 1956 Dihedral : 13.976 152.664 2053 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.42 % Allowed : 12.63 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1381 helix: 1.02 (0.25), residues: 442 sheet: 0.24 (0.30), residues: 280 loop : -1.37 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 166 TYR 0.012 0.001 TYR G 172 PHE 0.017 0.001 PHE B 159 TRP 0.009 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00305 (12094) covalent geometry : angle 0.52120 (16491) hydrogen bonds : bond 0.04134 ( 374) hydrogen bonds : angle 4.10949 ( 1028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9075 (mtm) cc_final: 0.7956 (ttm) REVERT: B 204 LYS cc_start: 0.7803 (tptt) cc_final: 0.7592 (tptt) REVERT: C 101 TYR cc_start: 0.7586 (m-80) cc_final: 0.6853 (m-10) REVERT: C 142 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7968 (tpt) REVERT: C 233 ASN cc_start: 0.7764 (m-40) cc_final: 0.7097 (t0) REVERT: C 287 ASN cc_start: 0.8910 (t0) cc_final: 0.8622 (t0) REVERT: D 90 LEU cc_start: 0.8557 (mp) cc_final: 0.8333 (mp) REVERT: D 248 MET cc_start: 0.5836 (mmm) cc_final: 0.5251 (mmt) REVERT: D 260 MET cc_start: 0.8265 (mtm) cc_final: 0.7771 (ptp) REVERT: A 96 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8726 (mtpp) REVERT: G 118 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7624 (ttm110) REVERT: G 180 VAL cc_start: 0.8413 (p) cc_final: 0.7996 (m) REVERT: G 209 ILE cc_start: 0.7620 (mt) cc_final: 0.7363 (mp) outliers start: 29 outliers final: 9 residues processed: 101 average time/residue: 0.5529 time to fit residues: 61.0414 Evaluate side-chains 88 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 139 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082745 restraints weight = 24792.535| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.28 r_work: 0.3193 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12094 Z= 0.203 Angle : 0.565 7.688 16491 Z= 0.297 Chirality : 0.043 0.137 1903 Planarity : 0.004 0.039 1956 Dihedral : 14.003 153.145 2051 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.51 % Allowed : 14.38 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.22), residues: 1381 helix: 0.96 (0.25), residues: 444 sheet: 0.10 (0.30), residues: 286 loop : -1.47 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 174 TYR 0.017 0.001 TYR G 172 PHE 0.017 0.002 PHE B 159 TRP 0.010 0.002 TRP G 199 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00476 (12094) covalent geometry : angle 0.56547 (16491) hydrogen bonds : bond 0.04879 ( 374) hydrogen bonds : angle 4.19041 ( 1028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9114 (mtm) cc_final: 0.8083 (ttm) REVERT: B 13 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8203 (pp20) REVERT: B 204 LYS cc_start: 0.7858 (tptt) cc_final: 0.7600 (tptt) REVERT: C 13 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: C 101 TYR cc_start: 0.7643 (m-80) cc_final: 0.6790 (m-10) REVERT: C 115 ASP cc_start: 0.8311 (t0) cc_final: 0.8085 (t0) REVERT: C 142 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7945 (tpt) REVERT: C 233 ASN cc_start: 0.7861 (m-40) cc_final: 0.7086 (t0) REVERT: C 276 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7192 (ttp-110) REVERT: D 248 MET cc_start: 0.5857 (mmm) cc_final: 0.5263 (mmt) REVERT: D 260 MET cc_start: 0.8343 (mtm) cc_final: 0.7952 (ptp) REVERT: A 13 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7851 (pp20) REVERT: A 96 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8739 (mtpp) REVERT: G 118 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7607 (ttm110) REVERT: G 166 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8476 (ttm110) REVERT: G 180 VAL cc_start: 0.7777 (p) cc_final: 0.7308 (m) REVERT: G 209 ILE cc_start: 0.7612 (mt) cc_final: 0.7366 (mp) REVERT: G 231 GLU cc_start: 0.8864 (tt0) cc_final: 0.8493 (tm-30) outliers start: 30 outliers final: 10 residues processed: 102 average time/residue: 0.5284 time to fit residues: 58.8650 Evaluate side-chains 90 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 93 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085208 restraints weight = 24662.528| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.30 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12094 Z= 0.113 Angle : 0.492 8.554 16491 Z= 0.258 Chirality : 0.041 0.134 1903 Planarity : 0.003 0.033 1956 Dihedral : 13.760 152.835 2051 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.01 % Allowed : 15.38 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1381 helix: 1.34 (0.25), residues: 442 sheet: 0.17 (0.30), residues: 296 loop : -1.28 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 174 TYR 0.010 0.001 TYR G 172 PHE 0.017 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00262 (12094) covalent geometry : angle 0.49235 (16491) hydrogen bonds : bond 0.03578 ( 374) hydrogen bonds : angle 3.85029 ( 1028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9000 (mtm) cc_final: 0.8029 (ttm) REVERT: B 13 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8021 (pp20) REVERT: B 124 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7553 (ptm) REVERT: B 142 MET cc_start: 0.8738 (ttt) cc_final: 0.8512 (ttt) REVERT: B 204 LYS cc_start: 0.7817 (tptt) cc_final: 0.7408 (tptt) REVERT: C 13 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7865 (pp20) REVERT: C 101 TYR cc_start: 0.7587 (m-80) cc_final: 0.6762 (m-80) REVERT: C 233 ASN cc_start: 0.7635 (m-40) cc_final: 0.7286 (t0) REVERT: C 276 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7217 (ttp-110) REVERT: D 248 MET cc_start: 0.5778 (mmm) cc_final: 0.5220 (mmt) REVERT: D 260 MET cc_start: 0.8247 (mtm) cc_final: 0.7982 (mtm) REVERT: A 13 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: A 96 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8721 (mtpp) REVERT: A 201 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7902 (t80) REVERT: G 114 ILE cc_start: 0.9081 (tt) cc_final: 0.8865 (pp) REVERT: G 118 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7590 (ttm110) REVERT: G 180 VAL cc_start: 0.8112 (p) cc_final: 0.7658 (m) REVERT: G 209 ILE cc_start: 0.7625 (mt) cc_final: 0.7380 (mp) REVERT: G 212 ILE cc_start: 0.7232 (mm) cc_final: 0.6987 (mm) REVERT: G 231 GLU cc_start: 0.8827 (tt0) cc_final: 0.8345 (tm-30) outliers start: 24 outliers final: 8 residues processed: 95 average time/residue: 0.5448 time to fit residues: 56.8856 Evaluate side-chains 90 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084266 restraints weight = 24812.243| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.31 r_work: 0.3223 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12094 Z= 0.137 Angle : 0.504 9.423 16491 Z= 0.263 Chirality : 0.042 0.133 1903 Planarity : 0.004 0.034 1956 Dihedral : 13.778 153.473 2051 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.34 % Allowed : 16.22 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.22), residues: 1381 helix: 1.39 (0.25), residues: 443 sheet: 0.17 (0.30), residues: 296 loop : -1.28 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 174 TYR 0.013 0.001 TYR G 172 PHE 0.016 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00320 (12094) covalent geometry : angle 0.50418 (16491) hydrogen bonds : bond 0.03950 ( 374) hydrogen bonds : angle 3.85306 ( 1028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9006 (mtm) cc_final: 0.7936 (ttm) REVERT: B 13 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: B 124 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7515 (ptm) REVERT: B 204 LYS cc_start: 0.7825 (tptt) cc_final: 0.7400 (tptt) REVERT: C 13 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7883 (pp20) REVERT: C 101 TYR cc_start: 0.7509 (m-80) cc_final: 0.6760 (m-80) REVERT: C 204 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8045 (tptm) REVERT: C 233 ASN cc_start: 0.7717 (m-40) cc_final: 0.7271 (t0) REVERT: C 276 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7099 (ttp-110) REVERT: D 248 MET cc_start: 0.5756 (mmm) cc_final: 0.5143 (mmt) REVERT: D 260 MET cc_start: 0.8303 (mtm) cc_final: 0.7998 (mtm) REVERT: A 96 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8707 (mtpp) REVERT: A 115 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: A 201 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7912 (t80) REVERT: G 114 ILE cc_start: 0.9075 (tt) cc_final: 0.8853 (pp) REVERT: G 118 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7570 (ttm110) REVERT: G 180 VAL cc_start: 0.8243 (p) cc_final: 0.7877 (m) REVERT: G 209 ILE cc_start: 0.7635 (mt) cc_final: 0.7384 (mp) REVERT: G 212 ILE cc_start: 0.7219 (mm) cc_final: 0.7006 (mm) REVERT: G 231 GLU cc_start: 0.8842 (tt0) cc_final: 0.8382 (tm-30) outliers start: 28 outliers final: 12 residues processed: 96 average time/residue: 0.5711 time to fit residues: 60.0744 Evaluate side-chains 96 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084501 restraints weight = 24758.522| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.29 r_work: 0.3230 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12094 Z= 0.135 Angle : 0.519 15.933 16491 Z= 0.265 Chirality : 0.042 0.132 1903 Planarity : 0.003 0.032 1956 Dihedral : 13.814 156.167 2051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.26 % Allowed : 16.47 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.22), residues: 1381 helix: 1.43 (0.25), residues: 442 sheet: 0.13 (0.30), residues: 296 loop : -1.25 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 174 TYR 0.012 0.001 TYR G 172 PHE 0.016 0.001 PHE B 159 TRP 0.009 0.001 TRP G 199 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00317 (12094) covalent geometry : angle 0.51862 (16491) hydrogen bonds : bond 0.03814 ( 374) hydrogen bonds : angle 3.82835 ( 1028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8991 (mtm) cc_final: 0.8070 (ttm) REVERT: B 13 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7937 (pp20) REVERT: B 124 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7506 (ptm) REVERT: B 204 LYS cc_start: 0.7840 (tptt) cc_final: 0.7397 (tptt) REVERT: C 13 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: C 101 TYR cc_start: 0.7532 (m-80) cc_final: 0.6825 (m-80) REVERT: C 204 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8066 (tptm) REVERT: C 233 ASN cc_start: 0.7663 (m-40) cc_final: 0.7264 (t0) REVERT: C 276 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7160 (ttp-110) REVERT: D 248 MET cc_start: 0.5729 (mmm) cc_final: 0.5319 (mpp) REVERT: D 260 MET cc_start: 0.8278 (mtm) cc_final: 0.7985 (mtm) REVERT: A 40 TYR cc_start: 0.8428 (p90) cc_final: 0.8151 (p90) REVERT: A 96 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8702 (mtpp) REVERT: A 112 MET cc_start: 0.8816 (mtp) cc_final: 0.8613 (mtm) REVERT: A 115 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: A 201 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7945 (t80) REVERT: G 114 ILE cc_start: 0.9167 (tt) cc_final: 0.8875 (pp) REVERT: G 118 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7567 (ttm110) REVERT: G 180 VAL cc_start: 0.8344 (p) cc_final: 0.7986 (m) REVERT: G 182 ARG cc_start: 0.6391 (pmt-80) cc_final: 0.6120 (pmt-80) REVERT: G 209 ILE cc_start: 0.7636 (mt) cc_final: 0.7384 (mp) REVERT: G 231 GLU cc_start: 0.8819 (tt0) cc_final: 0.8369 (tm-30) outliers start: 27 outliers final: 11 residues processed: 98 average time/residue: 0.5243 time to fit residues: 56.5615 Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 219 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081662 restraints weight = 25116.109| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.34 r_work: 0.3173 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12094 Z= 0.239 Angle : 0.615 13.812 16491 Z= 0.318 Chirality : 0.044 0.138 1903 Planarity : 0.004 0.038 1956 Dihedral : 14.126 161.482 2051 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.34 % Allowed : 17.47 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.22), residues: 1381 helix: 1.05 (0.25), residues: 444 sheet: -0.13 (0.30), residues: 296 loop : -1.47 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 174 TYR 0.019 0.002 TYR G 172 PHE 0.018 0.002 PHE B 159 TRP 0.012 0.002 TRP G 138 HIS 0.005 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00567 (12094) covalent geometry : angle 0.61513 (16491) hydrogen bonds : bond 0.05072 ( 374) hydrogen bonds : angle 4.21439 ( 1028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9125 (mtm) cc_final: 0.8021 (ttm) REVERT: B 13 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8083 (pp20) REVERT: B 204 LYS cc_start: 0.7968 (tptt) cc_final: 0.7601 (tptt) REVERT: C 101 TYR cc_start: 0.7493 (m-80) cc_final: 0.6800 (m-80) REVERT: C 204 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (tptm) REVERT: C 233 ASN cc_start: 0.8108 (m-40) cc_final: 0.7470 (t0) REVERT: D 223 ILE cc_start: 0.8734 (tp) cc_final: 0.8357 (pp) REVERT: D 248 MET cc_start: 0.5937 (mmm) cc_final: 0.5543 (mpp) REVERT: D 260 MET cc_start: 0.8333 (mtm) cc_final: 0.7999 (ptp) REVERT: A 40 TYR cc_start: 0.8447 (p90) cc_final: 0.8157 (p90) REVERT: A 96 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8672 (mtpp) REVERT: A 112 MET cc_start: 0.8851 (mtp) cc_final: 0.8623 (mtm) REVERT: G 118 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7567 (ttm110) REVERT: G 180 VAL cc_start: 0.8428 (p) cc_final: 0.8202 (m) REVERT: G 209 ILE cc_start: 0.7736 (mt) cc_final: 0.7476 (mp) REVERT: G 231 GLU cc_start: 0.8858 (tt0) cc_final: 0.8468 (tm-30) outliers start: 28 outliers final: 15 residues processed: 96 average time/residue: 0.5009 time to fit residues: 52.8334 Evaluate side-chains 93 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 131 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085243 restraints weight = 24482.299| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.27 r_work: 0.3245 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12094 Z= 0.114 Angle : 0.522 15.541 16491 Z= 0.269 Chirality : 0.042 0.171 1903 Planarity : 0.003 0.032 1956 Dihedral : 14.038 176.125 2051 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.34 % Allowed : 18.56 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1381 helix: 1.40 (0.26), residues: 442 sheet: -0.03 (0.30), residues: 295 loop : -1.28 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 174 TYR 0.011 0.001 TYR G 172 PHE 0.016 0.001 PHE B 159 TRP 0.008 0.001 TRP G 199 HIS 0.003 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00273 (12094) covalent geometry : angle 0.52165 (16491) hydrogen bonds : bond 0.03486 ( 374) hydrogen bonds : angle 3.87391 ( 1028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8976 (mtm) cc_final: 0.7964 (ttm) REVERT: B 13 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: B 124 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7657 (ptm) REVERT: B 204 LYS cc_start: 0.7876 (tptt) cc_final: 0.7449 (tptt) REVERT: C 13 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7831 (pp20) REVERT: C 101 TYR cc_start: 0.7481 (m-80) cc_final: 0.7172 (m-80) REVERT: C 233 ASN cc_start: 0.7575 (m-40) cc_final: 0.7292 (t0) REVERT: C 276 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7168 (ttp-110) REVERT: D 248 MET cc_start: 0.5688 (mmm) cc_final: 0.5278 (mpp) REVERT: D 260 MET cc_start: 0.8220 (mtm) cc_final: 0.7936 (mtm) REVERT: A 40 TYR cc_start: 0.8435 (p90) cc_final: 0.8162 (p90) REVERT: A 96 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8704 (mtpp) REVERT: G 118 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7509 (ttp-170) REVERT: G 180 VAL cc_start: 0.8491 (p) cc_final: 0.8222 (m) REVERT: G 209 ILE cc_start: 0.7659 (mt) cc_final: 0.7422 (mp) REVERT: G 231 GLU cc_start: 0.8809 (tt0) cc_final: 0.8351 (tm-30) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 0.5804 time to fit residues: 57.1990 Evaluate side-chains 87 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 276 ARG Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain G residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081952 restraints weight = 25059.642| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.30 r_work: 0.3179 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12094 Z= 0.232 Angle : 0.627 13.348 16491 Z= 0.325 Chirality : 0.044 0.208 1903 Planarity : 0.004 0.039 1956 Dihedral : 14.180 176.332 2051 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.51 % Allowed : 18.39 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1381 helix: 1.07 (0.25), residues: 444 sheet: -0.21 (0.30), residues: 290 loop : -1.44 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 174 TYR 0.017 0.002 TYR G 172 PHE 0.017 0.002 PHE B 159 TRP 0.011 0.002 TRP G 138 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00548 (12094) covalent geometry : angle 0.62705 (16491) hydrogen bonds : bond 0.04985 ( 374) hydrogen bonds : angle 4.22326 ( 1028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9106 (mtm) cc_final: 0.8222 (ttm) REVERT: B 13 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7952 (pp20) REVERT: B 204 LYS cc_start: 0.7974 (tptt) cc_final: 0.7624 (tptt) REVERT: C 13 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7928 (pp20) REVERT: C 101 TYR cc_start: 0.7462 (m-80) cc_final: 0.7175 (m-80) REVERT: C 233 ASN cc_start: 0.8072 (m-40) cc_final: 0.7471 (t0) REVERT: D 223 ILE cc_start: 0.8736 (tp) cc_final: 0.8370 (pp) REVERT: D 248 MET cc_start: 0.5954 (mmm) cc_final: 0.5547 (mpp) REVERT: D 260 MET cc_start: 0.8319 (mtm) cc_final: 0.8000 (ptp) REVERT: A 40 TYR cc_start: 0.8496 (p90) cc_final: 0.8193 (p90) REVERT: A 96 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8639 (mtpp) REVERT: G 114 ILE cc_start: 0.8917 (pp) cc_final: 0.8648 (pp) REVERT: G 118 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7553 (ttp-170) REVERT: G 180 VAL cc_start: 0.8528 (p) cc_final: 0.8254 (m) REVERT: G 209 ILE cc_start: 0.7766 (mt) cc_final: 0.7513 (mp) REVERT: G 231 GLU cc_start: 0.8824 (tt0) cc_final: 0.8397 (tm-30) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.5950 time to fit residues: 57.3360 Evaluate side-chains 90 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084709 restraints weight = 24689.826| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.27 r_work: 0.3239 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12094 Z= 0.125 Angle : 0.540 13.345 16491 Z= 0.279 Chirality : 0.042 0.212 1903 Planarity : 0.003 0.033 1956 Dihedral : 14.022 177.494 2051 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.17 % Allowed : 18.81 % Favored : 80.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1381 helix: 1.38 (0.26), residues: 442 sheet: -0.01 (0.31), residues: 279 loop : -1.30 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 174 TYR 0.012 0.001 TYR G 172 PHE 0.016 0.001 PHE B 159 TRP 0.007 0.001 TRP G 199 HIS 0.004 0.001 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00295 (12094) covalent geometry : angle 0.54006 (16491) hydrogen bonds : bond 0.03688 ( 374) hydrogen bonds : angle 3.94608 ( 1028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2894.65 seconds wall clock time: 50 minutes 24.46 seconds (3024.46 seconds total)