Starting phenix.real_space_refine on Tue Feb 3 18:28:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijs_60643/02_2026/9ijs_60643.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 18 5.16 5 C 3920 2.51 5 N 1009 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6074 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2083 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 280, 2083 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PHE:plan': 6, 'TYR:plan': 1, 'HIS:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2446 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 325} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 5, 'ASP:plan': 13, 'GLU:plan': 19, 'GLN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 215 Chain: "H" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1545 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 110 Time building chain proxies: 1.30, per 1000 atoms: 0.21 Number of scatterers: 6074 At special positions: 0 Unit cell: (76.544, 95.68, 133.12, 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 18 16.00 P 6 15.00 O 1121 8.00 N 1009 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 227 " distance=2.03 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: 0.36 Conformation dependent library (CDL) restraints added in 314.0 milliseconds 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 29.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 42 through 68 removed outlier: 4.133A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 104 removed outlier: 3.951A pdb=" N PHE A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 110 through 144 removed outlier: 3.813A pdb=" N CYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 179 Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 184 through 188 removed outlier: 4.224A pdb=" N GLY A 187 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 200 through 211 removed outlier: 4.206A pdb=" N GLY A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.588A pdb=" N PHE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 removed outlier: 4.305A pdb=" N VAL A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Proline residue: A 280 - end of helix removed outlier: 3.529A pdb=" N SER A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 321 removed outlier: 3.969A pdb=" N ASN A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.784A pdb=" N ARG A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.796A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.850A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 62 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.520A pdb=" N ALA C 201 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR C 186 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 188 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 197 " --> pdb=" O ARG C 188 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS C 198 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 218 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 270 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.947A pdb=" N VAL C 343 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 327 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 322 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 236 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 241 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.947A pdb=" N VAL C 343 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 327 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 322 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 236 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.540A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER H 55 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.540A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER H 55 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 144 through 146 removed outlier: 3.645A pdb=" N VAL H 158 " --> pdb=" O ILE H 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 149 through 151 removed outlier: 6.682A pdb=" N LEU H 150 " --> pdb=" O GLU H 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 192 through 193 removed outlier: 3.569A pdb=" N LYS H 184 " --> pdb=" O GLN H 176 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TRP H 174 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR H 188 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL H 172 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN H 228 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 236 " --> pdb=" O GLN H 229 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1893 1.34 - 1.46: 1484 1.46 - 1.58: 2797 1.58 - 1.69: 22 1.69 - 1.81: 21 Bond restraints: 6217 Sorted by residual: bond pdb=" OG1 TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" OG1 TPO A 490 " pdb=" P TPO A 490 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O3P TPO A 490 " pdb=" P TPO A 490 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O2P TPO A 490 " pdb=" P TPO A 490 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O3P TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 6212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 8429 2.57 - 5.14: 89 5.14 - 7.72: 21 7.72 - 10.29: 1 10.29 - 12.86: 3 Bond angle restraints: 8543 Sorted by residual: angle pdb=" OG1 TPO A 490 " pdb=" P TPO A 490 " pdb=" O1P TPO A 490 " ideal model delta sigma weight residual 100.43 113.29 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CB TPO A 491 " pdb=" OG1 TPO A 491 " pdb=" P TPO A 491 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA GLN H 229 " pdb=" CB GLN H 229 " pdb=" CG GLN H 229 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N SER A 77 " pdb=" CA SER A 77 " pdb=" C SER A 77 " ideal model delta sigma weight residual 113.18 108.62 4.56 1.33e+00 5.65e-01 1.18e+01 angle pdb=" CA LEU A 174 " pdb=" CB LEU A 174 " pdb=" CG LEU A 174 " ideal model delta sigma weight residual 116.30 127.83 -11.53 3.50e+00 8.16e-02 1.09e+01 ... (remaining 8538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3153 17.61 - 35.22: 349 35.22 - 52.83: 73 52.83 - 70.43: 12 70.43 - 88.04: 5 Dihedral angle restraints: 3592 sinusoidal: 1082 harmonic: 2510 Sorted by residual: dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual -86.00 -157.62 71.62 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CA HIS A 73 " pdb=" C HIS A 73 " pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA LEU A 211 " pdb=" C LEU A 211 " pdb=" N TYR A 212 " pdb=" CA TYR A 212 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 764 0.045 - 0.089: 194 0.089 - 0.134: 66 0.134 - 0.179: 10 0.179 - 0.223: 2 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CB VAL A 48 " pdb=" CA VAL A 48 " pdb=" CG1 VAL A 48 " pdb=" CG2 VAL A 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU A 59 " pdb=" CB LEU A 59 " pdb=" CD1 LEU A 59 " pdb=" CD2 LEU A 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE H 187 " pdb=" CA ILE H 187 " pdb=" CG1 ILE H 187 " pdb=" CG2 ILE H 187 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1033 not shown) Planarity restraints: 1061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 206 " 0.017 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE A 206 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 206 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 206 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 206 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 206 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 39 " -0.015 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP H 39 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP H 39 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 39 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 39 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 39 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 139 " -0.166 9.50e-02 1.11e+02 7.46e-02 3.60e+00 pdb=" NE ARG A 139 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 139 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 139 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 139 " -0.008 2.00e-02 2.50e+03 ... (remaining 1058 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 656 2.75 - 3.29: 6088 3.29 - 3.82: 10159 3.82 - 4.36: 10475 4.36 - 4.90: 18968 Nonbonded interactions: 46346 Sorted by model distance: nonbonded pdb=" O LYS C 195 " pdb=" OG1 THR C 224 " model vdw 2.210 3.040 nonbonded pdb=" O TRP A 192 " pdb=" OG SER A 196 " model vdw 2.241 3.040 nonbonded pdb=" OG SER H 20 " pdb=" O MET H 86 " model vdw 2.293 3.040 nonbonded pdb=" NZ LYS A 125 " pdb=" OG SER A 310 " model vdw 2.315 3.120 nonbonded pdb=" NE2 GLN H 177 " pdb=" O LYS H 181 " model vdw 2.334 3.120 ... (remaining 46341 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.420 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 0.110 6220 Z= 0.213 Angle : 0.733 12.859 8549 Z= 0.360 Chirality : 0.046 0.223 1036 Planarity : 0.004 0.075 1061 Dihedral : 15.638 88.042 1967 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.36 % Allowed : 35.70 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.30), residues: 835 helix: 0.53 (0.35), residues: 232 sheet: -1.02 (0.35), residues: 236 loop : -0.95 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.015 0.001 TYR H 63 PHE 0.043 0.002 PHE A 206 TRP 0.034 0.002 TRP H 39 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6217) covalent geometry : angle 0.73302 ( 8543) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.52179 ( 6) hydrogen bonds : bond 0.20810 ( 282) hydrogen bonds : angle 8.32186 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.157 Fit side-chains REVERT: A 316 ILE cc_start: 0.7739 (tt) cc_final: 0.7441 (tp) outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.0751 time to fit residues: 12.0540 Evaluate side-chains 120 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.159180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122330 restraints weight = 11247.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125841 restraints weight = 6514.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127728 restraints weight = 4733.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129286 restraints weight = 3998.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129875 restraints weight = 3580.813| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6220 Z= 0.151 Angle : 0.573 9.239 8549 Z= 0.300 Chirality : 0.043 0.140 1036 Planarity : 0.004 0.048 1061 Dihedral : 5.801 78.249 930 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.28 % Allowed : 33.15 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.30), residues: 835 helix: 0.60 (0.34), residues: 242 sheet: -1.19 (0.34), residues: 240 loop : -0.94 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.012 0.001 TYR H 107 PHE 0.023 0.001 PHE H 105 TRP 0.026 0.002 TRP H 39 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6217) covalent geometry : angle 0.57340 ( 8543) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.48103 ( 6) hydrogen bonds : bond 0.04278 ( 282) hydrogen bonds : angle 5.52200 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: H 73 ILE cc_start: 0.2329 (OUTLIER) cc_final: 0.1960 (mp) REVERT: H 101 ARG cc_start: 0.8279 (tmt170) cc_final: 0.8074 (tmt170) REVERT: H 212 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6925 (pt) outliers start: 29 outliers final: 22 residues processed: 148 average time/residue: 0.0665 time to fit residues: 13.2793 Evaluate side-chains 132 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124521 restraints weight = 11270.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127886 restraints weight = 6724.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130016 restraints weight = 5024.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131016 restraints weight = 4260.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131215 restraints weight = 3921.241| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6220 Z= 0.122 Angle : 0.547 9.294 8549 Z= 0.282 Chirality : 0.042 0.145 1036 Planarity : 0.003 0.032 1061 Dihedral : 5.601 78.353 929 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.38 % Allowed : 31.69 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.30), residues: 835 helix: 0.75 (0.33), residues: 244 sheet: -1.21 (0.34), residues: 231 loop : -0.99 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 307 TYR 0.011 0.001 TYR A 149 PHE 0.020 0.001 PHE H 105 TRP 0.025 0.002 TRP A 192 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6217) covalent geometry : angle 0.54698 ( 8543) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.87628 ( 6) hydrogen bonds : bond 0.03660 ( 282) hydrogen bonds : angle 4.86937 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.151 Fit side-chains REVERT: A 158 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6643 (mp) REVERT: A 185 TYR cc_start: 0.6901 (m-80) cc_final: 0.6593 (m-80) REVERT: A 285 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 236 ARG cc_start: 0.8638 (mtp85) cc_final: 0.8155 (mtp85) REVERT: H 21 LEU cc_start: 0.6284 (tt) cc_final: 0.6022 (tt) REVERT: H 73 ILE cc_start: 0.2234 (OUTLIER) cc_final: 0.1890 (mp) REVERT: H 101 ARG cc_start: 0.8229 (tmt170) cc_final: 0.8028 (tmt170) REVERT: H 177 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6759 (tp-100) REVERT: H 228 GLN cc_start: 0.9291 (pp30) cc_final: 0.9069 (tm-30) outliers start: 35 outliers final: 26 residues processed: 141 average time/residue: 0.0651 time to fit residues: 12.1418 Evaluate side-chains 143 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.159945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121851 restraints weight = 11351.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.125266 restraints weight = 6761.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127375 restraints weight = 5058.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128444 restraints weight = 4287.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129225 restraints weight = 3936.536| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6220 Z= 0.159 Angle : 0.557 8.785 8549 Z= 0.289 Chirality : 0.043 0.157 1036 Planarity : 0.004 0.050 1061 Dihedral : 5.666 77.715 929 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 8.56 % Allowed : 31.51 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.29), residues: 835 helix: 0.69 (0.33), residues: 243 sheet: -1.17 (0.34), residues: 230 loop : -0.96 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 200 TYR 0.016 0.001 TYR H 63 PHE 0.027 0.001 PHE H 105 TRP 0.015 0.002 TRP A 304 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6217) covalent geometry : angle 0.55734 ( 8543) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.73484 ( 6) hydrogen bonds : bond 0.03568 ( 282) hydrogen bonds : angle 4.75480 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.182 Fit side-chains REVERT: A 158 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6665 (mp) REVERT: A 285 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8222 (t80) REVERT: H 21 LEU cc_start: 0.6471 (tt) cc_final: 0.6206 (tt) REVERT: H 73 ILE cc_start: 0.2331 (OUTLIER) cc_final: 0.2020 (mp) REVERT: H 177 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6699 (tp-100) REVERT: H 228 GLN cc_start: 0.9331 (pp30) cc_final: 0.9119 (tm-30) outliers start: 47 outliers final: 36 residues processed: 144 average time/residue: 0.0594 time to fit residues: 11.4106 Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126072 restraints weight = 11382.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129580 restraints weight = 6661.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131442 restraints weight = 4912.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133008 restraints weight = 4187.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.133448 restraints weight = 3772.144| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6220 Z= 0.107 Angle : 0.538 9.016 8549 Z= 0.275 Chirality : 0.042 0.150 1036 Planarity : 0.003 0.033 1061 Dihedral : 5.489 78.484 929 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 8.38 % Allowed : 31.51 % Favored : 60.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.30), residues: 835 helix: 0.89 (0.33), residues: 243 sheet: -1.20 (0.34), residues: 233 loop : -0.81 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 307 TYR 0.012 0.001 TYR H 33 PHE 0.015 0.001 PHE H 105 TRP 0.032 0.002 TRP A 192 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6217) covalent geometry : angle 0.53784 ( 8543) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.95939 ( 6) hydrogen bonds : bond 0.03328 ( 282) hydrogen bonds : angle 4.44455 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.214 Fit side-chains REVERT: A 185 TYR cc_start: 0.6906 (m-80) cc_final: 0.6367 (m-80) REVERT: A 285 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8253 (t80) REVERT: C 198 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6830 (m-70) REVERT: C 236 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8176 (mtp85) REVERT: H 21 LEU cc_start: 0.6447 (tt) cc_final: 0.6211 (tt) REVERT: H 73 ILE cc_start: 0.1854 (OUTLIER) cc_final: 0.1513 (mp) REVERT: H 101 ARG cc_start: 0.8213 (tmt170) cc_final: 0.7989 (tmt170) REVERT: H 166 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8133 (tm-30) REVERT: H 177 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6679 (tp-100) REVERT: H 228 GLN cc_start: 0.9308 (pp30) cc_final: 0.9093 (tm-30) outliers start: 46 outliers final: 35 residues processed: 159 average time/residue: 0.0553 time to fit residues: 12.0563 Evaluate side-chains 156 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 177 GLN Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.157219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120077 restraints weight = 11127.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123430 restraints weight = 6589.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124837 restraints weight = 4893.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126565 restraints weight = 4241.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127205 restraints weight = 3811.901| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6220 Z= 0.214 Angle : 0.604 8.496 8549 Z= 0.315 Chirality : 0.044 0.162 1036 Planarity : 0.004 0.086 1061 Dihedral : 5.795 76.755 929 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 9.29 % Allowed : 31.15 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 835 helix: 0.63 (0.33), residues: 243 sheet: -1.24 (0.34), residues: 228 loop : -0.88 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 139 TYR 0.018 0.002 TYR H 33 PHE 0.032 0.002 PHE H 105 TRP 0.036 0.002 TRP A 192 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6217) covalent geometry : angle 0.60365 ( 8543) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.84962 ( 6) hydrogen bonds : bond 0.03738 ( 282) hydrogen bonds : angle 4.71064 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.186 Fit side-chains REVERT: A 78 TYR cc_start: 0.7926 (m-80) cc_final: 0.7615 (m-80) REVERT: A 185 TYR cc_start: 0.7001 (m-80) cc_final: 0.6465 (m-80) REVERT: A 285 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (t80) REVERT: C 198 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6655 (m-70) REVERT: H 73 ILE cc_start: 0.2630 (OUTLIER) cc_final: 0.2340 (mp) REVERT: H 166 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 51 outliers final: 39 residues processed: 150 average time/residue: 0.0521 time to fit residues: 10.7849 Evaluate side-chains 151 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 63 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.159491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122691 restraints weight = 11274.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125281 restraints weight = 6747.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126348 restraints weight = 5076.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126621 restraints weight = 4994.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126567 restraints weight = 4568.452| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6220 Z= 0.154 Angle : 0.585 8.638 8549 Z= 0.302 Chirality : 0.043 0.155 1036 Planarity : 0.004 0.065 1061 Dihedral : 5.739 77.898 929 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 8.20 % Allowed : 32.79 % Favored : 59.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.29), residues: 835 helix: 0.57 (0.33), residues: 246 sheet: -1.26 (0.34), residues: 228 loop : -0.91 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.017 0.001 TYR H 33 PHE 0.026 0.002 PHE H 105 TRP 0.048 0.002 TRP A 192 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6217) covalent geometry : angle 0.58482 ( 8543) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.88726 ( 6) hydrogen bonds : bond 0.03641 ( 282) hydrogen bonds : angle 4.61450 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.211 Fit side-chains REVERT: A 185 TYR cc_start: 0.6809 (m-80) cc_final: 0.6166 (m-80) REVERT: C 198 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6709 (m-70) REVERT: C 236 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8127 (mtp85) REVERT: H 73 ILE cc_start: 0.2474 (OUTLIER) cc_final: 0.2160 (mp) REVERT: H 101 ARG cc_start: 0.8274 (tmt170) cc_final: 0.8025 (tmt170) REVERT: H 166 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8223 (tm-30) outliers start: 45 outliers final: 40 residues processed: 145 average time/residue: 0.0615 time to fit residues: 12.2796 Evaluate side-chains 158 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.160976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124205 restraints weight = 10994.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127728 restraints weight = 6423.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129899 restraints weight = 4726.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130773 restraints weight = 3968.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131738 restraints weight = 3649.863| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6220 Z= 0.129 Angle : 0.579 10.180 8549 Z= 0.296 Chirality : 0.043 0.153 1036 Planarity : 0.003 0.035 1061 Dihedral : 5.583 78.057 929 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 7.65 % Allowed : 33.52 % Favored : 58.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.30), residues: 835 helix: 0.67 (0.33), residues: 248 sheet: -1.30 (0.34), residues: 228 loop : -0.92 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.014 0.001 TYR H 33 PHE 0.023 0.001 PHE A 206 TRP 0.062 0.002 TRP A 192 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6217) covalent geometry : angle 0.57865 ( 8543) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.98594 ( 6) hydrogen bonds : bond 0.03409 ( 282) hydrogen bonds : angle 4.49790 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.192 Fit side-chains REVERT: A 185 TYR cc_start: 0.6868 (m-80) cc_final: 0.6327 (m-80) REVERT: C 198 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6590 (m-70) REVERT: C 236 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8214 (mtp85) REVERT: H 73 ILE cc_start: 0.2409 (OUTLIER) cc_final: 0.2123 (mp) REVERT: H 228 GLN cc_start: 0.9380 (pp30) cc_final: 0.9176 (tm-30) outliers start: 42 outliers final: 38 residues processed: 151 average time/residue: 0.0607 time to fit residues: 12.2634 Evaluate side-chains 159 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125167 restraints weight = 11415.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127069 restraints weight = 6498.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127937 restraints weight = 5247.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128029 restraints weight = 4937.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128620 restraints weight = 4626.299| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6220 Z= 0.131 Angle : 0.590 8.899 8549 Z= 0.302 Chirality : 0.043 0.158 1036 Planarity : 0.003 0.034 1061 Dihedral : 5.558 77.515 929 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 7.83 % Allowed : 34.06 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 835 helix: 0.63 (0.33), residues: 244 sheet: -1.27 (0.33), residues: 234 loop : -0.84 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 307 TYR 0.026 0.001 TYR H 63 PHE 0.022 0.002 PHE H 105 TRP 0.061 0.002 TRP A 192 HIS 0.001 0.000 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6217) covalent geometry : angle 0.58975 ( 8543) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.87004 ( 6) hydrogen bonds : bond 0.03423 ( 282) hydrogen bonds : angle 4.48666 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.206 Fit side-chains REVERT: A 73 HIS cc_start: 0.7812 (t-90) cc_final: 0.7411 (t-90) REVERT: A 185 TYR cc_start: 0.6731 (m-80) cc_final: 0.6220 (m-80) REVERT: A 285 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8162 (t80) REVERT: C 99 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8571 (tpm170) REVERT: C 198 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6748 (m-70) REVERT: C 236 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8142 (mtp85) REVERT: H 73 ILE cc_start: 0.2581 (OUTLIER) cc_final: 0.2264 (mp) REVERT: H 228 GLN cc_start: 0.9380 (pp30) cc_final: 0.9177 (tm-30) outliers start: 43 outliers final: 38 residues processed: 147 average time/residue: 0.0621 time to fit residues: 12.3648 Evaluate side-chains 157 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125233 restraints weight = 11123.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127285 restraints weight = 6525.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.128403 restraints weight = 5229.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129103 restraints weight = 4694.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128871 restraints weight = 4414.786| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6220 Z= 0.136 Angle : 0.599 8.859 8549 Z= 0.306 Chirality : 0.043 0.151 1036 Planarity : 0.003 0.034 1061 Dihedral : 5.537 77.092 929 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 8.01 % Allowed : 33.33 % Favored : 58.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.29), residues: 835 helix: 0.49 (0.32), residues: 250 sheet: -1.29 (0.33), residues: 234 loop : -0.88 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 200 TYR 0.012 0.001 TYR H 63 PHE 0.022 0.001 PHE H 105 TRP 0.064 0.002 TRP A 192 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6217) covalent geometry : angle 0.59882 ( 8543) SS BOND : bond 0.00234 ( 3) SS BOND : angle 0.84151 ( 6) hydrogen bonds : bond 0.03407 ( 282) hydrogen bonds : angle 4.47839 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1670 Ramachandran restraints generated. 835 Oldfield, 0 Emsley, 835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.214 Fit side-chains REVERT: A 73 HIS cc_start: 0.7784 (t-90) cc_final: 0.7390 (t-90) REVERT: A 185 TYR cc_start: 0.6759 (m-80) cc_final: 0.6198 (m-80) REVERT: C 99 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8561 (tpm170) REVERT: C 198 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6729 (m-70) REVERT: C 236 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8144 (mtp85) REVERT: H 73 ILE cc_start: 0.2742 (OUTLIER) cc_final: 0.2457 (mp) REVERT: H 228 GLN cc_start: 0.9373 (pp30) cc_final: 0.9173 (tm-30) outliers start: 44 outliers final: 40 residues processed: 149 average time/residue: 0.0572 time to fit residues: 11.4888 Evaluate side-chains 160 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 198 HIS Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 67 optimal weight: 0.0370 chunk 40 optimal weight: 0.0470 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.2494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128606 restraints weight = 11028.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132329 restraints weight = 6196.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.134691 restraints weight = 4428.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135836 restraints weight = 3660.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136770 restraints weight = 3313.252| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6220 Z= 0.107 Angle : 0.587 9.065 8549 Z= 0.297 Chirality : 0.043 0.167 1036 Planarity : 0.003 0.030 1061 Dihedral : 5.351 77.381 929 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.01 % Allowed : 35.88 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 835 helix: 0.66 (0.32), residues: 249 sheet: -1.30 (0.33), residues: 235 loop : -0.86 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 307 TYR 0.007 0.001 TYR H 33 PHE 0.021 0.001 PHE A 206 TRP 0.059 0.002 TRP A 192 HIS 0.001 0.000 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6217) covalent geometry : angle 0.58643 ( 8543) SS BOND : bond 0.00331 ( 3) SS BOND : angle 0.83455 ( 6) hydrogen bonds : bond 0.03221 ( 282) hydrogen bonds : angle 4.34270 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.78 seconds wall clock time: 19 minutes 7.01 seconds (1147.01 seconds total)