Starting phenix.real_space_refine on Tue Aug 4 21:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.cif Found real_map, /net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.map" model { file = "/net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22gl_68263/08_2026/22gl_68263.cif" } resolution = 3.3 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= 0.001 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 5 5.49 5 S 29 5.16 5 C 4275 2.51 5 N 1107 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6624 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 181 Classifications: {'peptide': 27} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2268 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 272} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2470 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 304} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 1.11, per 1000 atoms: 0.17 Number of scatterers: 6624 At special positions: 0 Unit cell: (84.63, 100.44, 153.45, 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 29 16.00 P 5 15.00 O 1208 8.00 N 1107 7.00 C 4275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.02 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.02 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: 0.35 Conformation dependent library (CDL) restraints added in 298.6 milliseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 33.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'R' and resid 35 through 63 removed outlier: 3.814A pdb=" N ALA R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 88 Processing helix chain 'R' and resid 88 through 98 removed outlier: 3.501A pdb=" N LEU R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 139 Proline residue: R 113 - end of helix removed outlier: 3.508A pdb=" N ILE R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 148 removed outlier: 4.524A pdb=" N ASN R 146 " --> pdb=" O ILE R 142 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 147 " --> pdb=" O TRP R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 174 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 211 Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 237 through 268 Proline residue: R 257 - end of helix removed outlier: 3.687A pdb=" N ILE R 263 " --> pdb=" O GLN R 259 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER R 266 " --> pdb=" O GLY R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 289 removed outlier: 4.640A pdb=" N SER R 283 " --> pdb=" O LYS R 279 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 287 " --> pdb=" O SER R 283 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA R 289 " --> pdb=" O CYS R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 302 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 306 through 313 Processing helix chain 'H' and resid 64 through 69 removed outlier: 4.351A pdb=" N GLY H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.219A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.075A pdb=" N HIS A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing sheet with id=AA1, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA2, first strand: chain 'R' and resid 339 through 340 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.240A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.240A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.467A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.467A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.246A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 80 " --> pdb=" O CYS A 59 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.905A pdb=" N LEU A 287 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.133A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 981 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: 0.70 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1871 1.33 - 1.48: 2117 1.48 - 1.63: 2751 1.63 - 1.78: 13 1.78 - 1.93: 25 Bond restraints: 6777 Sorted by residual: bond pdb=" OG1 TPO R 339 " pdb=" P TPO R 339 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO R 342 " pdb=" P TPO R 342 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO R 336 " pdb=" P TPO R 336 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O2P SEP R 338 " pdb=" P SEP R 338 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O2P SEP R 334 " pdb=" P SEP R 334 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 6772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 8421 2.64 - 5.28: 737 5.28 - 7.92: 82 7.92 - 10.56: 8 10.56 - 13.20: 3 Bond angle restraints: 9251 Sorted by residual: angle pdb=" CA ILE R 169 " pdb=" C ILE R 169 " pdb=" N PRO R 170 " ideal model delta sigma weight residual 120.83 117.60 3.23 6.10e-01 2.69e+00 2.80e+01 angle pdb=" N ILE R 91 " pdb=" CA ILE R 91 " pdb=" C ILE R 91 " ideal model delta sigma weight residual 110.82 106.00 4.82 9.70e-01 1.06e+00 2.47e+01 angle pdb=" C VAL L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.78 124.88 -5.10 1.03e+00 9.43e-01 2.45e+01 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 114.67 109.27 5.40 1.10e+00 8.26e-01 2.41e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.14 105.90 5.24 1.08e+00 8.57e-01 2.35e+01 ... (remaining 9246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 3814 15.75 - 31.49: 137 31.49 - 47.24: 25 47.24 - 62.99: 15 62.99 - 78.73: 8 Dihedral angle restraints: 3999 sinusoidal: 1473 harmonic: 2526 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 57.71 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" C PHE A 149 " pdb=" N PHE A 149 " pdb=" CA PHE A 149 " pdb=" CB PHE A 149 " ideal model delta harmonic sigma weight residual -122.60 -113.45 -9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C LEU A 100 " pdb=" N LEU A 100 " pdb=" CA LEU A 100 " pdb=" CB LEU A 100 " ideal model delta harmonic sigma weight residual -122.60 -114.03 -8.57 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 3996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 767 0.077 - 0.154: 247 0.154 - 0.230: 61 0.230 - 0.307: 8 0.307 - 0.384: 5 Chirality restraints: 1088 Sorted by residual: chirality pdb=" CG LEU R 89 " pdb=" CB LEU R 89 " pdb=" CD1 LEU R 89 " pdb=" CD2 LEU R 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB VAL H 5 " pdb=" CA VAL H 5 " pdb=" CG1 VAL H 5 " pdb=" CG2 VAL H 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.99 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA LYS A 284 " pdb=" N LYS A 284 " pdb=" C LYS A 284 " pdb=" CB LYS A 284 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1085 not shown) Planarity restraints: 1151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.056 2.00e-02 2.50e+03 2.87e-02 1.65e+01 pdb=" CG TYR L 92 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 192 " -0.050 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR R 192 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 192 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 192 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR R 192 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR R 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 192 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 192 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 240 " 0.018 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASP A 240 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP A 240 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 241 " 0.020 2.00e-02 2.50e+03 ... (remaining 1148 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2605 2.87 - 3.38: 6442 3.38 - 3.88: 11478 3.88 - 4.39: 13257 4.39 - 4.90: 21613 Nonbonded interactions: 55395 Sorted by model distance: nonbonded pdb=" O SER R 95 " pdb=" N HIS R 100 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP H 76 " pdb=" NZ LYS H 79 " model vdw 2.440 3.120 nonbonded pdb=" OE1 GLU A 145 " pdb=" NE ARG A 165 " model vdw 2.450 3.120 nonbonded pdb=" O TRP R 102 " pdb=" N PHE R 104 " model vdw 2.460 3.120 nonbonded pdb=" N ASP A 29 " pdb=" O VAL A 171 " model vdw 2.466 3.120 ... (remaining 55390 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.330 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: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.017 0.120 6780 Z= 0.937 Angle : 1.562 13.200 9257 Z= 1.016 Chirality : 0.081 0.384 1088 Planarity : 0.008 0.074 1151 Dihedral : 10.219 78.733 2358 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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 (0.29), residues: 838 helix: -1.13 (0.30), residues: 249 sheet: 0.95 (0.32), residues: 257 loop : -1.27 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 236 TYR 0.056 0.007 TYR L 92 PHE 0.033 0.004 PHE C 51 TRP 0.036 0.006 TRP R 102 HIS 0.008 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.01744 / 0.94 ( 6777) covalent geometry : angle 1.56091 / 1.02 ( 9251) SS BOND : bond 0.00828 / 0.37 ( 3) SS BOND : angle 2.78122 / 1.38 ( 6) hydrogen bonds : bond 0.17859 / 12.40 ( 351) hydrogen bonds : angle 8.23500 / 6.01 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 115 LEU cc_start: 0.8027 (mt) cc_final: 0.7747 (tp) REVERT: H 63 TYR cc_start: 0.8397 (m-80) cc_final: 0.8079 (m-80) REVERT: H 115 GLN cc_start: 0.7329 (mm-40) cc_final: 0.7082 (mm-40) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0773 time to fit residues: 16.6047 Evaluate side-chains 129 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 98 GLN R 292 ASN A 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.201742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158690 restraints weight = 7730.299| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.23 r_work: 0.3406 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6780 Z= 0.230 Angle : 0.700 11.087 9257 Z= 0.367 Chirality : 0.047 0.152 1088 Planarity : 0.006 0.067 1151 Dihedral : 6.956 85.958 944 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 10.53 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.25 (0.29), residues: 838 helix: 0.55 (0.32), residues: 252 sheet: 1.22 (0.34), residues: 246 loop : -0.89 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.017 0.002 TYR L 92 PHE 0.021 0.002 PHE H 105 TRP 0.018 0.002 TRP H 50 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 ( 6777) covalent geometry : angle 0.69929 / 0.37 ( 9251) SS BOND : bond 0.00323 / 0.16 ( 3) SS BOND : angle 1.42815 / 0.77 ( 6) hydrogen bonds : bond 0.04925 / 3.43 ( 351) hydrogen bonds : angle 5.93400 / 4.36 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 163 LEU cc_start: 0.8346 (mt) cc_final: 0.8060 (mp) REVERT: R 186 VAL cc_start: 0.7774 (t) cc_final: 0.7142 (m) REVERT: R 228 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7583 (mmm160) REVERT: R 232 ARG cc_start: 0.4101 (ttp-170) cc_final: 0.2857 (tmm-80) REVERT: R 264 MET cc_start: 0.7944 (mtp) cc_final: 0.7733 (mtp) REVERT: H 10 SER cc_start: 0.8345 (p) cc_final: 0.8089 (m) REVERT: H 63 TYR cc_start: 0.8698 (m-80) cc_final: 0.8447 (m-80) REVERT: H 115 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7721 (mm-40) REVERT: L 4 GLN cc_start: 0.8236 (pt0) cc_final: 0.8007 (pt0) REVERT: A 31 ILE cc_start: 0.5803 (pt) cc_final: 0.5536 (pt) outliers start: 13 outliers final: 6 residues processed: 155 average time/residue: 0.0771 time to fit residues: 15.2003 Evaluate side-chains 132 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain A residue 56 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.221430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.176870 restraints weight = 8350.770| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.85 r_work: 0.3658 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6780 Z= 0.194 Angle : 0.623 7.003 9257 Z= 0.322 Chirality : 0.045 0.138 1088 Planarity : 0.005 0.048 1151 Dihedral : 6.467 85.934 944 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.03 % Allowed : 11.69 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.27 (0.29), residues: 838 helix: 0.85 (0.32), residues: 253 sheet: 0.85 (0.33), residues: 257 loop : -0.85 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 7 TYR 0.016 0.001 TYR L 92 PHE 0.024 0.002 PHE H 105 TRP 0.015 0.002 TRP R 74 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 6777) covalent geometry : angle 0.62304 / 0.32 ( 9251) SS BOND : bond 0.00072 / 0.03 ( 3) SS BOND : angle 0.98658 / 0.52 ( 6) hydrogen bonds : bond 0.04398 / 3.09 ( 351) hydrogen bonds : angle 5.40820 / 3.99 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 200 ARG cc_start: 0.6133 (mpt-90) cc_final: 0.4894 (mmt90) REVERT: R 223 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8340 (p) REVERT: R 228 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7493 (tpt90) REVERT: H 63 TYR cc_start: 0.8818 (m-80) cc_final: 0.8527 (m-80) REVERT: L 4 GLN cc_start: 0.8041 (pt0) cc_final: 0.7827 (pt0) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.0784 time to fit residues: 13.0883 Evaluate side-chains 118 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.213539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170756 restraints weight = 8037.296| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.46 r_work: 0.3687 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6780 Z= 0.155 Angle : 0.581 7.468 9257 Z= 0.297 Chirality : 0.043 0.135 1088 Planarity : 0.005 0.048 1151 Dihedral : 6.321 87.074 944 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.45 % Allowed : 14.14 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.37 (0.29), residues: 838 helix: 0.91 (0.32), residues: 252 sheet: 0.81 (0.33), residues: 265 loop : -0.72 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 7 TYR 0.013 0.001 TYR L 92 PHE 0.016 0.001 PHE H 105 TRP 0.014 0.001 TRP R 74 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 6777) covalent geometry : angle 0.58058 / 0.30 ( 9251) SS BOND : bond 0.00027 / 0.01 ( 3) SS BOND : angle 0.62900 / 0.33 ( 6) hydrogen bonds : bond 0.03947 / 2.76 ( 351) hydrogen bonds : angle 5.09683 / 3.79 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 142 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8301 (mt) REVERT: R 163 LEU cc_start: 0.8329 (mt) cc_final: 0.8012 (mp) REVERT: R 200 ARG cc_start: 0.6273 (mpt-90) cc_final: 0.4976 (mmt90) REVERT: R 228 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7394 (tpt90) REVERT: R 253 ILE cc_start: 0.8042 (mt) cc_final: 0.7822 (mm) REVERT: H 63 TYR cc_start: 0.8747 (m-80) cc_final: 0.8505 (m-80) REVERT: A 160 LYS cc_start: 0.8331 (mttt) cc_final: 0.8067 (ttpt) outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 0.0892 time to fit residues: 14.7230 Evaluate side-chains 127 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain A residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 82 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 0.4980 chunk 80 optimal weight: 0.0870 chunk 45 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158540 restraints weight = 7631.145| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.87 r_work: 0.3390 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6780 Z= 0.116 Angle : 0.546 6.408 9257 Z= 0.275 Chirality : 0.042 0.131 1088 Planarity : 0.004 0.045 1151 Dihedral : 6.037 84.255 944 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.03 % Allowed : 12.84 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.61 (0.29), residues: 838 helix: 1.16 (0.33), residues: 252 sheet: 0.99 (0.33), residues: 264 loop : -0.66 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 312 TYR 0.009 0.001 TYR L 92 PHE 0.010 0.001 PHE H 105 TRP 0.020 0.001 TRP R 74 HIS 0.002 0.000 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 6777) covalent geometry : angle 0.54619 / 0.28 ( 9251) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.47016 / 0.25 ( 6) hydrogen bonds : bond 0.03763 / 2.56 ( 351) hydrogen bonds : angle 4.79671 / 3.60 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 148 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.6643 (ttm-80) REVERT: R 163 LEU cc_start: 0.8334 (mt) cc_final: 0.7997 (mp) REVERT: R 165 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7090 (mt) REVERT: R 200 ARG cc_start: 0.6394 (mpt-90) cc_final: 0.5040 (mmt90) REVERT: R 223 THR cc_start: 0.8691 (m) cc_final: 0.8287 (p) REVERT: R 228 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7533 (tpt90) REVERT: R 253 ILE cc_start: 0.8160 (mt) cc_final: 0.7921 (mm) REVERT: H 63 TYR cc_start: 0.8756 (m-80) cc_final: 0.8541 (m-80) REVERT: A 160 LYS cc_start: 0.8401 (mttt) cc_final: 0.7990 (ttpt) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.0865 time to fit residues: 15.1713 Evaluate side-chains 134 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 140 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.199702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160726 restraints weight = 7771.926| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.91 r_work: 0.3346 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6780 Z= 0.173 Angle : 0.601 7.664 9257 Z= 0.303 Chirality : 0.044 0.145 1088 Planarity : 0.005 0.045 1151 Dihedral : 6.072 84.575 944 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 12.99 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.49 (0.29), residues: 838 helix: 1.16 (0.32), residues: 254 sheet: 0.74 (0.33), residues: 267 loop : -0.66 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 312 TYR 0.015 0.001 TYR L 92 PHE 0.020 0.001 PHE H 105 TRP 0.015 0.001 TRP R 74 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 6777) covalent geometry : angle 0.60085 / 0.30 ( 9251) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.70534 / 0.36 ( 6) hydrogen bonds : bond 0.03793 / 2.64 ( 351) hydrogen bonds : angle 4.92084 / 3.68 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7783 (tp) cc_final: 0.7269 (mt) REVERT: R 197 ARG cc_start: 0.7760 (ppt170) cc_final: 0.7428 (pmt-80) REVERT: R 200 ARG cc_start: 0.6436 (mpt-90) cc_final: 0.4965 (mmt90) REVERT: R 223 THR cc_start: 0.8729 (m) cc_final: 0.8333 (p) REVERT: R 228 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7523 (tpt90) REVERT: R 253 ILE cc_start: 0.8170 (mt) cc_final: 0.7952 (mm) REVERT: H 63 TYR cc_start: 0.8783 (m-80) cc_final: 0.8555 (m-80) REVERT: A 31 ILE cc_start: 0.7596 (mm) cc_final: 0.7383 (mm) REVERT: A 160 LYS cc_start: 0.8472 (mttt) cc_final: 0.8240 (ttpt) outliers start: 18 outliers final: 15 residues processed: 128 average time/residue: 0.0864 time to fit residues: 14.2081 Evaluate side-chains 124 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 ARG Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 44 optimal weight: 0.0770 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.199958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160737 restraints weight = 7652.234| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.90 r_work: 0.3340 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6780 Z= 0.156 Angle : 0.566 7.085 9257 Z= 0.286 Chirality : 0.043 0.141 1088 Planarity : 0.005 0.056 1151 Dihedral : 5.952 80.600 944 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.89 % Allowed : 13.71 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 838 helix: 1.29 (0.33), residues: 254 sheet: 0.74 (0.33), residues: 264 loop : -0.76 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 312 TYR 0.012 0.001 TYR L 92 PHE 0.016 0.001 PHE H 105 TRP 0.018 0.001 TRP R 74 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6777) covalent geometry : angle 0.56549 / 0.29 ( 9251) SS BOND : bond 0.00074 / 0.03 ( 3) SS BOND : angle 0.59434 / 0.31 ( 6) hydrogen bonds : bond 0.03674 / 2.55 ( 351) hydrogen bonds : angle 4.79515 / 3.60 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 163 LEU cc_start: 0.8336 (mt) cc_final: 0.8011 (mp) REVERT: R 165 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7308 (mt) REVERT: R 223 THR cc_start: 0.8643 (m) cc_final: 0.8433 (t) REVERT: R 228 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7535 (tpt90) REVERT: R 253 ILE cc_start: 0.8147 (mt) cc_final: 0.7922 (mm) REVERT: R 267 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: H 63 TYR cc_start: 0.8769 (m-80) cc_final: 0.8565 (m-80) REVERT: L 5 MET cc_start: 0.8997 (mmm) cc_final: 0.8719 (mtp) REVERT: A 160 LYS cc_start: 0.8453 (mttt) cc_final: 0.8253 (ttpt) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.0760 time to fit residues: 12.7764 Evaluate side-chains 125 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 140 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.159841 restraints weight = 7701.106| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.99 r_work: 0.3283 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6780 Z= 0.162 Angle : 0.576 7.630 9257 Z= 0.291 Chirality : 0.043 0.140 1088 Planarity : 0.005 0.044 1151 Dihedral : 5.795 76.666 944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.03 % Allowed : 14.00 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 838 helix: 1.34 (0.33), residues: 255 sheet: 0.66 (0.33), residues: 264 loop : -0.80 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 7 TYR 0.013 0.001 TYR L 92 PHE 0.018 0.001 PHE H 105 TRP 0.017 0.001 TRP R 74 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6777) covalent geometry : angle 0.57583 / 0.29 ( 9251) SS BOND : bond 0.00040 / 0.02 ( 3) SS BOND : angle 0.66360 / 0.34 ( 6) hydrogen bonds : bond 0.03626 / 2.50 ( 351) hydrogen bonds : angle 4.77635 / 3.58 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: R 140 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7541 (mmtt) REVERT: R 163 LEU cc_start: 0.8369 (mt) cc_final: 0.8058 (mp) REVERT: R 165 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7261 (mt) REVERT: R 223 THR cc_start: 0.8617 (m) cc_final: 0.8392 (t) REVERT: R 228 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7559 (tpt90) REVERT: R 253 ILE cc_start: 0.8197 (mt) cc_final: 0.7958 (mm) REVERT: R 267 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: L 5 MET cc_start: 0.8996 (mmm) cc_final: 0.8738 (mtp) outliers start: 21 outliers final: 19 residues processed: 115 average time/residue: 0.0696 time to fit residues: 10.5631 Evaluate side-chains 121 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157083 restraints weight = 7660.471| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.10 r_work: 0.3467 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6780 Z= 0.175 Angle : 0.588 8.089 9257 Z= 0.294 Chirality : 0.044 0.242 1088 Planarity : 0.004 0.047 1151 Dihedral : 5.768 74.726 944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.17 % Allowed : 14.14 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.30), residues: 838 helix: 1.45 (0.33), residues: 256 sheet: 0.57 (0.33), residues: 267 loop : -0.76 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 285 TYR 0.014 0.001 TYR L 92 PHE 0.018 0.001 PHE H 105 TRP 0.016 0.001 TRP R 74 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 6777) covalent geometry : angle 0.58751 / 0.29 ( 9251) SS BOND : bond 0.00047 / 0.02 ( 3) SS BOND : angle 0.62896 / 0.32 ( 6) hydrogen bonds : bond 0.03620 / 2.52 ( 351) hydrogen bonds : angle 4.79806 / 3.61 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: R 163 LEU cc_start: 0.8352 (mt) cc_final: 0.7973 (mp) REVERT: R 165 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7282 (mt) REVERT: R 223 THR cc_start: 0.8657 (m) cc_final: 0.8431 (t) REVERT: R 253 ILE cc_start: 0.8221 (mt) cc_final: 0.7997 (mm) REVERT: R 267 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: L 5 MET cc_start: 0.9012 (mmm) cc_final: 0.8771 (mtp) outliers start: 22 outliers final: 18 residues processed: 119 average time/residue: 0.0760 time to fit residues: 11.9745 Evaluate side-chains 124 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 42 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.186597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144913 restraints weight = 7777.073| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.45 r_work: 0.3244 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6780 Z= 0.133 Angle : 0.580 10.953 9257 Z= 0.284 Chirality : 0.043 0.214 1088 Planarity : 0.005 0.049 1151 Dihedral : 5.633 75.492 944 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.45 % Allowed : 15.15 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.56 (0.30), residues: 838 helix: 1.47 (0.33), residues: 251 sheet: 0.65 (0.33), residues: 267 loop : -0.71 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 62 TYR 0.010 0.001 TYR L 92 PHE 0.013 0.001 PHE H 105 TRP 0.018 0.001 TRP R 74 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6777) covalent geometry : angle 0.58017 / 0.28 ( 9251) SS BOND : bond 0.00038 / 0.02 ( 3) SS BOND : angle 0.46158 / 0.24 ( 6) hydrogen bonds : bond 0.03451 / 2.39 ( 351) hydrogen bonds : angle 4.69582 / 3.54 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.259 Fit side-chains REVERT: R 140 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7368 (mtmm) REVERT: R 163 LEU cc_start: 0.8346 (mt) cc_final: 0.8096 (mp) REVERT: R 165 LEU cc_start: 0.7740 (tp) cc_final: 0.7284 (mt) REVERT: R 253 ILE cc_start: 0.8158 (mt) cc_final: 0.7938 (mm) REVERT: R 265 MET cc_start: 0.7810 (tmm) cc_final: 0.7548 (tmm) REVERT: R 267 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: L 5 MET cc_start: 0.9186 (mmm) cc_final: 0.8923 (mtp) REVERT: L 75 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8614 (p) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.0744 time to fit residues: 12.5598 Evaluate side-chains 129 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 PHE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 250 SER Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 67 HIS ** 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 = 0.4066 r_free = 0.4066 target = 0.184791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141882 restraints weight = 7654.783| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.61 r_work: 0.3228 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6780 Z= 0.169 Angle : 0.604 9.818 9257 Z= 0.300 Chirality : 0.044 0.234 1088 Planarity : 0.004 0.049 1151 Dihedral : 5.707 76.121 944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.45 % Allowed : 15.73 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.49 (0.29), residues: 838 helix: 1.56 (0.33), residues: 251 sheet: 0.55 (0.33), residues: 267 loop : -0.83 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 62 TYR 0.014 0.001 TYR L 92 PHE 0.019 0.001 PHE H 105 TRP 0.016 0.001 TRP R 74 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6777) covalent geometry : angle 0.60380 / 0.30 ( 9251) SS BOND : bond 0.00050 / 0.03 ( 3) SS BOND : angle 0.62985 / 0.32 ( 6) hydrogen bonds : bond 0.03524 / 2.46 ( 351) hydrogen bonds : angle 4.74991 / 3.58 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.04 seconds wall clock time: 29 minutes 34.37 seconds (1774.37 seconds total)