Starting phenix.real_space_refine on Tue Mar 3 20:11:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.map" model { file = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y12_33554/03_2026/7y12_33554.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5431 2.51 5 N 1454 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8501 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1654 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2553 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2053 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BAL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'PLM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.20, per 1000 atoms: 0.26 Number of scatterers: 8501 At special positions: 0 Unit cell: (122.85, 84.375, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1547 8.00 N 1454 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.64 Conformation dependent library (CDL) restraints added in 237.1 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.038A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.158A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.503A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.537A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.686A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.583A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 23 through 52 Processing helix chain 'R' and resid 62 through 88 Processing helix chain 'R' and resid 92 through 129 removed outlier: 3.949A pdb=" N LYS R 96 " --> pdb=" O ASN R 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 171 through 189 Processing helix chain 'R' and resid 189 through 209 removed outlier: 3.564A pdb=" N SER R 209 " --> pdb=" O VAL R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 244 removed outlier: 3.983A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 247 No H-bonds generated for 'chain 'R' and resid 245 through 247' Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.408A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.651A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.802A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.507A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.551A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.596A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.929A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.915A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.752A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1230 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: 1.43 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2292 1.33 - 1.45: 1585 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8676 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.306 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.508 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.512 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C LEU R 235 " pdb=" N PRO R 236 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 8671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 11614 2.21 - 4.41: 122 4.41 - 6.62: 14 6.62 - 8.83: 5 8.83 - 11.04: 1 Bond angle restraints: 11756 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.33 7.47 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CB MET R 42 " pdb=" CG MET R 42 " pdb=" SD MET R 42 " ideal model delta sigma weight residual 112.70 123.74 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MET R 42 " pdb=" CB MET R 42 " pdb=" CG MET R 42 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.25e+00 angle pdb=" N MET R 42 " pdb=" CA MET R 42 " pdb=" CB MET R 42 " ideal model delta sigma weight residual 110.30 114.67 -4.37 1.54e+00 4.22e-01 8.03e+00 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4517 17.97 - 35.93: 479 35.93 - 53.90: 110 53.90 - 71.86: 13 71.86 - 89.83: 12 Dihedral angle restraints: 5131 sinusoidal: 1912 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 63.90 29.10 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP B 303 " pdb=" CB ASP B 303 " pdb=" CG ASP B 303 " pdb=" OD1 ASP B 303 " ideal model delta sinusoidal sigma weight residual -30.00 -88.66 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 808 0.028 - 0.056: 355 0.056 - 0.085: 112 0.085 - 0.113: 67 0.113 - 0.141: 15 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1354 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.010 2.00e-02 2.50e+03 9.66e-03 1.87e+00 pdb=" CG TYR B 105 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 236 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 240 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C TYR R 240 " 0.023 2.00e-02 2.50e+03 pdb=" O TYR R 240 " -0.008 2.00e-02 2.50e+03 pdb=" N TRP R 241 " -0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 124 2.65 - 3.21: 7641 3.21 - 3.77: 13387 3.77 - 4.34: 18365 4.34 - 4.90: 30773 Nonbonded interactions: 70290 Sorted by model distance: nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.086 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.147 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.187 3.120 nonbonded pdb=" OD1 ASN A 241 " pdb=" OH TYR A 287 " model vdw 2.213 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.262 3.040 ... (remaining 70285 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8678 Z= 0.153 Angle : 0.581 11.036 11760 Z= 0.295 Chirality : 0.040 0.141 1357 Planarity : 0.003 0.033 1468 Dihedral : 15.813 89.828 3043 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.22 % Allowed : 15.96 % Favored : 83.82 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.86 (0.27), residues: 1093 helix: 2.18 (0.28), residues: 361 sheet: -0.05 (0.32), residues: 271 loop : -0.27 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.024 0.002 TYR B 105 PHE 0.019 0.001 PHE R 75 TRP 0.016 0.001 TRP R 144 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8676) covalent geometry : angle 0.58090 (11756) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.80415 ( 4) hydrogen bonds : bond 0.17284 ( 430) hydrogen bonds : angle 6.50641 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.354 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.0900 time to fit residues: 18.1462 Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.169869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135637 restraints weight = 10501.780| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.06 r_work: 0.3398 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8678 Z= 0.174 Angle : 0.566 5.466 11760 Z= 0.306 Chirality : 0.042 0.165 1357 Planarity : 0.004 0.033 1468 Dihedral : 6.076 59.908 1242 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 16.18 % Favored : 81.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1093 helix: 2.17 (0.27), residues: 369 sheet: -0.11 (0.32), residues: 266 loop : -0.38 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.021 0.002 TYR B 105 PHE 0.019 0.002 PHE R 75 TRP 0.021 0.002 TRP R 144 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8676) covalent geometry : angle 0.56613 (11756) SS BOND : bond 0.00575 ( 2) SS BOND : angle 1.14897 ( 4) hydrogen bonds : bond 0.04457 ( 430) hydrogen bonds : angle 5.16972 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.328 Fit side-chains REVERT: A 328 ASP cc_start: 0.6724 (m-30) cc_final: 0.6514 (m-30) REVERT: A 333 GLN cc_start: 0.7290 (tm-30) cc_final: 0.6998 (mt0) REVERT: R 95 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5772 (t70) outliers start: 18 outliers final: 10 residues processed: 159 average time/residue: 0.0904 time to fit residues: 20.4186 Evaluate side-chains 153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.169096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134439 restraints weight = 10409.342| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.06 r_work: 0.3390 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8678 Z= 0.146 Angle : 0.529 6.817 11760 Z= 0.285 Chirality : 0.041 0.155 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.788 57.984 1239 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.03 % Allowed : 17.30 % Favored : 79.66 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.26), residues: 1093 helix: 2.20 (0.27), residues: 375 sheet: -0.16 (0.32), residues: 263 loop : -0.39 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.014 0.002 TYR B 105 PHE 0.017 0.001 PHE R 75 TRP 0.019 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8676) covalent geometry : angle 0.52842 (11756) SS BOND : bond 0.00504 ( 2) SS BOND : angle 1.01636 ( 4) hydrogen bonds : bond 0.04068 ( 430) hydrogen bonds : angle 4.94413 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.303 Fit side-chains REVERT: A 5 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 328 ASP cc_start: 0.6686 (m-30) cc_final: 0.6368 (m-30) REVERT: A 333 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6961 (mt0) REVERT: B 105 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7701 (t80) REVERT: R 95 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.5664 (t70) REVERT: R 156 MET cc_start: 0.7910 (mmm) cc_final: 0.7611 (mmt) outliers start: 27 outliers final: 16 residues processed: 159 average time/residue: 0.0842 time to fit residues: 19.0429 Evaluate side-chains 156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134228 restraints weight = 10593.601| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.08 r_work: 0.3388 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8678 Z= 0.144 Angle : 0.528 5.794 11760 Z= 0.283 Chirality : 0.041 0.156 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.761 57.508 1239 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.37 % Allowed : 18.09 % Favored : 78.54 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.26), residues: 1093 helix: 2.21 (0.27), residues: 375 sheet: -0.19 (0.32), residues: 263 loop : -0.43 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.015 0.002 TYR B 105 PHE 0.020 0.001 PHE R 75 TRP 0.018 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8676) covalent geometry : angle 0.52768 (11756) SS BOND : bond 0.00498 ( 2) SS BOND : angle 1.05841 ( 4) hydrogen bonds : bond 0.03942 ( 430) hydrogen bonds : angle 4.88426 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.303 Fit side-chains REVERT: A 5 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7322 (mp) REVERT: A 328 ASP cc_start: 0.6638 (m-30) cc_final: 0.6352 (m-30) REVERT: A 333 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6985 (mt0) REVERT: B 105 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 134 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6666 (ttp-110) REVERT: R 95 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5715 (t70) REVERT: R 156 MET cc_start: 0.7906 (mmm) cc_final: 0.7646 (mmt) REVERT: S 46 GLU cc_start: 0.7512 (pt0) cc_final: 0.7218 (pt0) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.0850 time to fit residues: 19.8184 Evaluate side-chains 162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.168477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133480 restraints weight = 10632.882| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.10 r_work: 0.3380 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8678 Z= 0.158 Angle : 0.548 9.771 11760 Z= 0.291 Chirality : 0.042 0.159 1357 Planarity : 0.004 0.032 1468 Dihedral : 5.878 59.099 1239 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.49 % Allowed : 17.64 % Favored : 77.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.71 (0.26), residues: 1093 helix: 2.19 (0.27), residues: 375 sheet: -0.25 (0.32), residues: 263 loop : -0.49 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.016 0.002 TYR B 105 PHE 0.020 0.002 PHE R 75 TRP 0.019 0.002 TRP R 144 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8676) covalent geometry : angle 0.54736 (11756) SS BOND : bond 0.00510 ( 2) SS BOND : angle 1.12238 ( 4) hydrogen bonds : bond 0.04022 ( 430) hydrogen bonds : angle 4.87226 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7345 (mp) REVERT: A 328 ASP cc_start: 0.6775 (m-30) cc_final: 0.6481 (m-30) REVERT: A 333 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: B 105 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7920 (t80) REVERT: B 134 ARG cc_start: 0.7176 (ttp80) cc_final: 0.6696 (ttp-110) REVERT: R 95 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5718 (t70) REVERT: S 46 GLU cc_start: 0.7495 (pt0) cc_final: 0.7160 (pt0) REVERT: S 113 GLN cc_start: 0.6845 (mm-40) cc_final: 0.6543 (mm-40) outliers start: 40 outliers final: 24 residues processed: 171 average time/residue: 0.0774 time to fit residues: 18.7313 Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 56 MET Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.0060 chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 58 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.171837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137307 restraints weight = 10394.436| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.08 r_work: 0.3438 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8678 Z= 0.099 Angle : 0.490 9.100 11760 Z= 0.258 Chirality : 0.039 0.152 1357 Planarity : 0.003 0.033 1468 Dihedral : 5.188 58.834 1239 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.37 % Allowed : 19.44 % Favored : 77.19 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.97 (0.26), residues: 1093 helix: 2.47 (0.28), residues: 377 sheet: -0.14 (0.32), residues: 263 loop : -0.40 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.010 0.001 TYR B 105 PHE 0.014 0.001 PHE R 75 TRP 0.020 0.001 TRP R 144 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8676) covalent geometry : angle 0.49016 (11756) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.88466 ( 4) hydrogen bonds : bond 0.03370 ( 430) hydrogen bonds : angle 4.62185 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7265 (mp) REVERT: A 328 ASP cc_start: 0.6593 (m-30) cc_final: 0.6177 (m-30) REVERT: A 333 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.7009 (mt0) REVERT: R 51 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6439 (mp) REVERT: R 156 MET cc_start: 0.7877 (mmm) cc_final: 0.7630 (mmt) REVERT: S 46 GLU cc_start: 0.7389 (pt0) cc_final: 0.7081 (pt0) REVERT: S 113 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6503 (mm-40) outliers start: 30 outliers final: 21 residues processed: 170 average time/residue: 0.0902 time to fit residues: 21.3885 Evaluate side-chains 166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137393 restraints weight = 10593.656| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.08 r_work: 0.3428 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8678 Z= 0.109 Angle : 0.501 8.424 11760 Z= 0.263 Chirality : 0.040 0.157 1357 Planarity : 0.003 0.032 1468 Dihedral : 5.184 58.558 1239 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.48 % Allowed : 19.66 % Favored : 76.85 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.00 (0.26), residues: 1093 helix: 2.46 (0.27), residues: 378 sheet: -0.09 (0.32), residues: 263 loop : -0.38 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.011 0.001 TYR B 105 PHE 0.017 0.001 PHE R 75 TRP 0.018 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8676) covalent geometry : angle 0.50053 (11756) SS BOND : bond 0.00442 ( 2) SS BOND : angle 1.13854 ( 4) hydrogen bonds : bond 0.03437 ( 430) hydrogen bonds : angle 4.58936 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7236 (mp) REVERT: A 197 LYS cc_start: 0.8105 (mttm) cc_final: 0.7863 (mttm) REVERT: A 328 ASP cc_start: 0.6608 (m-30) cc_final: 0.6254 (m-30) REVERT: A 333 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: R 51 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6473 (mp) REVERT: R 156 MET cc_start: 0.7879 (mmm) cc_final: 0.7648 (mmt) REVERT: S 46 GLU cc_start: 0.7333 (pt0) cc_final: 0.7024 (pt0) REVERT: S 47 TRP cc_start: 0.7682 (t60) cc_final: 0.7482 (t60) outliers start: 31 outliers final: 23 residues processed: 168 average time/residue: 0.0843 time to fit residues: 20.2542 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.173116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138873 restraints weight = 10444.806| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.08 r_work: 0.3449 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8678 Z= 0.097 Angle : 0.492 8.075 11760 Z= 0.258 Chirality : 0.039 0.152 1357 Planarity : 0.003 0.034 1468 Dihedral : 4.991 58.755 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.71 % Allowed : 19.89 % Favored : 76.40 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.27), residues: 1093 helix: 2.55 (0.27), residues: 379 sheet: -0.02 (0.32), residues: 264 loop : -0.38 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.012 0.001 TYR A 320 PHE 0.016 0.001 PHE R 75 TRP 0.019 0.001 TRP R 144 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8676) covalent geometry : angle 0.49204 (11756) SS BOND : bond 0.00428 ( 2) SS BOND : angle 1.11838 ( 4) hydrogen bonds : bond 0.03272 ( 430) hydrogen bonds : angle 4.48813 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 333 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6905 (mt0) REVERT: R 51 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6474 (mp) REVERT: R 156 MET cc_start: 0.7866 (mmm) cc_final: 0.7624 (mmt) REVERT: S 46 GLU cc_start: 0.7286 (pt0) cc_final: 0.6992 (pt0) REVERT: S 47 TRP cc_start: 0.7606 (t60) cc_final: 0.7362 (t60) outliers start: 33 outliers final: 25 residues processed: 168 average time/residue: 0.0828 time to fit residues: 19.8335 Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.167866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133379 restraints weight = 10551.357| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.06 r_work: 0.3377 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8678 Z= 0.188 Angle : 0.586 8.484 11760 Z= 0.310 Chirality : 0.043 0.165 1357 Planarity : 0.004 0.037 1468 Dihedral : 5.983 58.754 1239 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.71 % Allowed : 20.00 % Favored : 76.29 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.77 (0.26), residues: 1093 helix: 2.19 (0.27), residues: 376 sheet: -0.10 (0.32), residues: 265 loop : -0.50 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 168 TYR 0.019 0.002 TYR B 105 PHE 0.024 0.002 PHE R 75 TRP 0.020 0.002 TRP R 144 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8676) covalent geometry : angle 0.58500 (11756) SS BOND : bond 0.00474 ( 2) SS BOND : angle 1.67942 ( 4) hydrogen bonds : bond 0.04168 ( 430) hydrogen bonds : angle 4.83649 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 328 ASP cc_start: 0.6742 (m-30) cc_final: 0.6417 (m-30) REVERT: B 105 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 134 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6749 (ttp-110) REVERT: R 51 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6706 (mp) REVERT: S 46 GLU cc_start: 0.7463 (pt0) cc_final: 0.7136 (pt0) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.0896 time to fit residues: 22.0188 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135157 restraints weight = 10528.217| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.08 r_work: 0.3400 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8678 Z= 0.137 Angle : 0.550 10.673 11760 Z= 0.289 Chirality : 0.041 0.160 1357 Planarity : 0.004 0.045 1468 Dihedral : 5.642 57.187 1239 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.26 % Allowed : 20.67 % Favored : 76.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.26), residues: 1093 helix: 2.26 (0.27), residues: 377 sheet: -0.11 (0.32), residues: 263 loop : -0.50 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 168 TYR 0.014 0.002 TYR B 105 PHE 0.020 0.001 PHE R 75 TRP 0.020 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8676) covalent geometry : angle 0.54962 (11756) SS BOND : bond 0.00484 ( 2) SS BOND : angle 1.48348 ( 4) hydrogen bonds : bond 0.03784 ( 430) hydrogen bonds : angle 4.72278 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 328 ASP cc_start: 0.6616 (m-30) cc_final: 0.6284 (m-30) REVERT: B 105 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 134 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6743 (ttp-110) REVERT: R 51 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6594 (mp) REVERT: S 46 GLU cc_start: 0.7375 (pt0) cc_final: 0.7075 (pt0) outliers start: 29 outliers final: 22 residues processed: 163 average time/residue: 0.0874 time to fit residues: 20.1204 Evaluate side-chains 167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 285 HIS Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 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 = 0.3937 r_free = 0.3937 target = 0.170838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136347 restraints weight = 10536.404| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.08 r_work: 0.3411 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8678 Z= 0.117 Angle : 0.532 9.632 11760 Z= 0.279 Chirality : 0.041 0.158 1357 Planarity : 0.003 0.040 1468 Dihedral : 5.495 56.488 1239 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.15 % Allowed : 20.67 % Favored : 76.18 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.33 % 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 (0.26), residues: 1093 helix: 2.38 (0.27), residues: 377 sheet: -0.08 (0.32), residues: 263 loop : -0.48 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 168 TYR 0.012 0.001 TYR A 320 PHE 0.018 0.001 PHE R 75 TRP 0.020 0.001 TRP R 144 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8676) covalent geometry : angle 0.53186 (11756) SS BOND : bond 0.00458 ( 2) SS BOND : angle 1.31136 ( 4) hydrogen bonds : bond 0.03585 ( 430) hydrogen bonds : angle 4.63885 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.34 seconds wall clock time: 42 minutes 18.67 seconds (2538.67 seconds total)