Starting phenix.real_space_refine on Wed Feb 4 11:07:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pmk_71738/02_2026/9pmk_71738.map" } resolution = 2.84 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= 0.003 sd= 0.026 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 12 5.49 5 S 48 5.16 5 C 6232 2.51 5 N 1760 2.21 5 O 2008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10060 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2483 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2483 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2483 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2483 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.18 Number of scatterers: 10060 At special positions: 0 Unit cell: (78.09, 101.928, 160.29, 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 48 16.00 P 12 15.00 O 2008 8.00 N 1760 7.00 C 6232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 46.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 74 through 89 Proline residue: C 83 - end of helix Processing helix chain 'C' and resid 105 through 121 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.538A pdb=" N GLY C 170 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 192 Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 208 through 214 removed outlier: 4.319A pdb=" N VAL C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.624A pdb=" N LYS C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 303 Processing helix chain 'C' and resid 311 through 318 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 22 through 28 removed outlier: 3.509A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 74 through 89 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 105 through 120 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 167 through 171 removed outlier: 3.544A pdb=" N GLY B 170 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 192 Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 208 through 214 removed outlier: 4.303A pdb=" N VAL B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.569A pdb=" N LYS B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 303 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 74 through 89 Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 105 through 120 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.512A pdb=" N GLY A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 192 Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.608A pdb=" N LYS A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 303 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 74 through 89 Proline residue: D 83 - end of helix Processing helix chain 'D' and resid 105 through 120 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 167 through 171 removed outlier: 3.539A pdb=" N GLY D 170 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 192 Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.590A pdb=" N LYS D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'D' and resid 311 through 318 Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 55 removed outlier: 8.051A pdb=" N TYR C 54 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR C 35 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 6 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 34 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE C 8 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C 36 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA C 10 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS C 7 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL C 98 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP C 9 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N SER C 100 " --> pdb=" O TRP C 9 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL C 11 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 124 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N SER C 162 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS C 126 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS C 164 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 128 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR C 163 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR C 224 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 13.631A pdb=" N MET C 165 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 18.795A pdb=" N MET C 226 " --> pdb=" O MET C 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 55 removed outlier: 8.127A pdb=" N TYR B 54 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B 35 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 6 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR B 34 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 8 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 36 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA B 10 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N HIS B 7 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL B 98 " --> pdb=" O HIS B 7 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP B 9 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N SER B 100 " --> pdb=" O TRP B 9 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL B 11 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 124 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N SER B 162 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B 126 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS B 164 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 128 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 163 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N THR B 224 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 13.633A pdb=" N MET B 165 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 18.801A pdb=" N MET B 226 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 239 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 8.130A pdb=" N TYR A 54 " --> pdb=" O MET A 33 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 35 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 6 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR A 34 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 8 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 36 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA A 10 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A 100 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 124 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N SER A 162 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS A 126 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 239 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 55 removed outlier: 8.139A pdb=" N TYR D 54 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR D 35 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL D 6 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR D 34 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE D 8 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL D 36 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA D 10 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS D 7 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 98 " --> pdb=" O HIS D 7 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP D 9 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N SER D 100 " --> pdb=" O TRP D 9 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL D 11 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 124 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N SER D 162 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS D 126 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS D 164 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 128 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR D 163 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N THR D 224 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 13.639A pdb=" N MET D 165 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 18.784A pdb=" N MET D 226 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 239 " --> pdb=" O LEU D 278 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1395 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: 1.17 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3448 1.34 - 1.47: 2274 1.47 - 1.59: 4426 1.59 - 1.72: 12 1.72 - 1.84: 76 Bond restraints: 10236 Sorted by residual: bond pdb=" CG LEU C 148 " pdb=" CD1 LEU C 148 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.22e-01 bond pdb=" CG LEU B 148 " pdb=" CD1 LEU B 148 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.98e-01 bond pdb=" CG1 ILE D 128 " pdb=" CD1 ILE D 128 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.96e-01 bond pdb=" CG1 ILE C 128 " pdb=" CD1 ILE C 128 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.92e-01 bond pdb=" CG1 ILE B 128 " pdb=" CD1 ILE B 128 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.82e-01 ... (remaining 10231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 13626 1.17 - 2.33: 182 2.33 - 3.50: 50 3.50 - 4.67: 1 4.67 - 5.83: 9 Bond angle restraints: 13868 Sorted by residual: angle pdb=" CA HIS C 209 " pdb=" C HIS C 209 " pdb=" N PRO C 210 " ideal model delta sigma weight residual 118.44 122.32 -3.88 1.59e+00 3.96e-01 5.95e+00 angle pdb=" N HIS C 209 " pdb=" CA HIS C 209 " pdb=" C HIS C 209 " ideal model delta sigma weight residual 109.81 114.93 -5.12 2.21e+00 2.05e-01 5.38e+00 angle pdb=" CA HIS C 209 " pdb=" C HIS C 209 " pdb=" O HIS C 209 " ideal model delta sigma weight residual 120.16 117.57 2.59 1.37e+00 5.33e-01 3.58e+00 angle pdb=" C LYS A 246 " pdb=" N ASP A 247 " pdb=" CA ASP A 247 " ideal model delta sigma weight residual 122.82 124.98 -2.16 1.42e+00 4.96e-01 2.31e+00 angle pdb=" C LYS D 246 " pdb=" N ASP D 247 " pdb=" CA ASP D 247 " ideal model delta sigma weight residual 122.82 124.97 -2.15 1.42e+00 4.96e-01 2.30e+00 ... (remaining 13863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 5689 13.18 - 26.36: 371 26.36 - 39.54: 93 39.54 - 52.72: 24 52.72 - 65.90: 19 Dihedral angle restraints: 6196 sinusoidal: 2508 harmonic: 3688 Sorted by residual: dihedral pdb=" N GLN B 5 " pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " ideal model delta sinusoidal sigma weight residual -60.00 -119.98 59.98 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN C 5 " pdb=" CA GLN C 5 " pdb=" CB GLN C 5 " pdb=" CG GLN C 5 " ideal model delta sinusoidal sigma weight residual -60.00 -119.87 59.87 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG D 143 " pdb=" CA ARG D 143 " pdb=" CB ARG D 143 " pdb=" CG ARG D 143 " ideal model delta sinusoidal sigma weight residual -60.00 -119.79 59.79 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 984 0.031 - 0.062: 402 0.062 - 0.093: 71 0.093 - 0.124: 79 0.124 - 0.155: 4 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA HIS A 209 " pdb=" N HIS A 209 " pdb=" C HIS A 209 " pdb=" CB HIS A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA HIS D 209 " pdb=" N HIS D 209 " pdb=" C HIS D 209 " pdb=" CB HIS D 209 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA HIS B 209 " pdb=" N HIS B 209 " pdb=" C HIS B 209 " pdb=" CB HIS B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1537 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 143 " -0.167 9.50e-02 1.11e+02 7.49e-02 3.56e+00 pdb=" NE ARG C 143 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG C 143 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 143 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 143 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " -0.142 9.50e-02 1.11e+02 6.38e-02 2.67e+00 pdb=" NE ARG B 143 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 110 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO C 111 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " -0.021 5.00e-02 4.00e+02 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 6486 3.04 - 3.50: 10259 3.50 - 3.97: 15840 3.97 - 4.43: 19550 4.43 - 4.90: 30342 Nonbonded interactions: 82477 Sorted by model distance: nonbonded pdb=" C4 G2P C 501 " pdb=" N1 G2P C 501 " model vdw 2.575 2.672 nonbonded pdb=" C4 G2P D 501 " pdb=" N1 G2P D 501 " model vdw 2.575 2.672 nonbonded pdb=" C4 G2P B 501 " pdb=" N1 G2P B 501 " model vdw 2.575 2.672 nonbonded pdb=" C4 G2P A 501 " pdb=" N1 G2P A 501 " model vdw 2.576 2.672 nonbonded pdb=" N THR C 218 " pdb=" O THR C 218 " model vdw 2.633 2.496 ... (remaining 82472 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.880 Find NCS groups from input model: 0.180 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 : 0.004 0.031 10236 Z= 0.163 Angle : 0.411 5.832 13868 Z= 0.215 Chirality : 0.041 0.155 1540 Planarity : 0.004 0.075 1820 Dihedral : 10.429 65.898 3836 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.03 % Allowed : 4.40 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.24), residues: 1296 helix: 1.13 (0.22), residues: 596 sheet: 1.21 (0.34), residues: 300 loop : 0.09 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 143 TYR 0.008 0.001 TYR C 35 PHE 0.008 0.001 PHE C 263 TRP 0.005 0.001 TRP C 9 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00376 (10236) covalent geometry : angle 0.41056 (13868) hydrogen bonds : bond 0.16662 ( 478) hydrogen bonds : angle 7.29692 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.236 Fit side-chains REVERT: B 161 VAL cc_start: 0.9161 (t) cc_final: 0.8948 (m) REVERT: A 62 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8420 (ttp-110) REVERT: A 143 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.4731 (mmm160) REVERT: A 174 GLN cc_start: 0.9033 (tp40) cc_final: 0.8808 (tp40) REVERT: A 325 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6557 (pp) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.7892 time to fit residues: 98.9672 Evaluate side-chains 67 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 209 HIS C 306 GLN B 81 GLN B 164 HIS B 195 ASN B 209 HIS B 223 ASN B 306 GLN A 81 GLN A 164 HIS A 209 HIS A 223 ASN D 81 GLN D 164 HIS D 195 ASN D 209 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054881 restraints weight = 22016.205| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.95 r_work: 0.2788 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10236 Z= 0.213 Angle : 0.507 6.238 13868 Z= 0.269 Chirality : 0.043 0.157 1540 Planarity : 0.004 0.038 1820 Dihedral : 8.482 65.216 1538 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.62 % Allowed : 9.55 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.24), residues: 1296 helix: 1.66 (0.22), residues: 572 sheet: 1.28 (0.34), residues: 300 loop : 0.25 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 44 TYR 0.023 0.002 TYR C 258 PHE 0.012 0.001 PHE C 240 TRP 0.005 0.001 TRP A 9 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00487 (10236) covalent geometry : angle 0.50662 (13868) hydrogen bonds : bond 0.04541 ( 478) hydrogen bonds : angle 5.32261 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.285 Fit side-chains REVERT: B 161 VAL cc_start: 0.9171 (t) cc_final: 0.8948 (m) REVERT: A 62 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8410 (ttp-110) REVERT: A 143 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.4632 (mmm160) REVERT: A 174 GLN cc_start: 0.8897 (tp40) cc_final: 0.8675 (tp-100) outliers start: 28 outliers final: 8 residues processed: 91 average time/residue: 0.7261 time to fit residues: 69.9471 Evaluate side-chains 62 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 223 ASN C 306 GLN B 81 GLN A 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056813 restraints weight = 21700.534| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.88 r_work: 0.2836 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10236 Z= 0.122 Angle : 0.436 5.981 13868 Z= 0.233 Chirality : 0.041 0.152 1540 Planarity : 0.003 0.037 1820 Dihedral : 8.241 64.358 1535 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.22 % Allowed : 11.05 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.25), residues: 1296 helix: 2.01 (0.22), residues: 572 sheet: 1.23 (0.34), residues: 304 loop : 0.35 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 44 TYR 0.025 0.001 TYR C 258 PHE 0.010 0.001 PHE C 240 TRP 0.005 0.001 TRP A 9 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00277 (10236) covalent geometry : angle 0.43620 (13868) hydrogen bonds : bond 0.03708 ( 478) hydrogen bonds : angle 4.75244 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.253 Fit side-chains REVERT: B 161 VAL cc_start: 0.9150 (t) cc_final: 0.8937 (m) REVERT: A 62 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8422 (ttp-110) REVERT: A 143 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.4648 (mmm160) REVERT: A 174 GLN cc_start: 0.8837 (tp40) cc_final: 0.8632 (tp-100) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.6867 time to fit residues: 57.4882 Evaluate side-chains 66 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 0.0050 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 HIS B 81 GLN B 306 GLN A 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059111 restraints weight = 21740.025| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.89 r_work: 0.2890 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10236 Z= 0.091 Angle : 0.407 5.888 13868 Z= 0.218 Chirality : 0.040 0.144 1540 Planarity : 0.003 0.041 1820 Dihedral : 7.863 63.594 1532 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.31 % Allowed : 11.70 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.25), residues: 1296 helix: 2.29 (0.22), residues: 572 sheet: 1.37 (0.34), residues: 300 loop : 0.34 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 62 TYR 0.015 0.001 TYR B 258 PHE 0.009 0.001 PHE C 240 TRP 0.004 0.001 TRP A 9 HIS 0.003 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00201 (10236) covalent geometry : angle 0.40712 (13868) hydrogen bonds : bond 0.03237 ( 478) hydrogen bonds : angle 4.34718 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.290 Fit side-chains REVERT: C 85 ILE cc_start: 0.9415 (mt) cc_final: 0.9207 (mp) REVERT: B 161 VAL cc_start: 0.9158 (t) cc_final: 0.8947 (m) REVERT: A 62 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8424 (ttp-110) REVERT: A 143 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.4591 (mmm160) outliers start: 14 outliers final: 5 residues processed: 90 average time/residue: 0.6337 time to fit residues: 60.6034 Evaluate side-chains 70 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057631 restraints weight = 21991.665| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.95 r_work: 0.2855 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10236 Z= 0.127 Angle : 0.431 6.014 13868 Z= 0.229 Chirality : 0.041 0.149 1540 Planarity : 0.003 0.042 1820 Dihedral : 7.810 63.689 1529 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.50 % Allowed : 12.92 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.25), residues: 1296 helix: 2.30 (0.22), residues: 572 sheet: 1.44 (0.34), residues: 300 loop : 0.35 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 62 TYR 0.030 0.001 TYR B 258 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP A 9 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00298 (10236) covalent geometry : angle 0.43145 (13868) hydrogen bonds : bond 0.03352 ( 478) hydrogen bonds : angle 4.36335 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.251 Fit side-chains REVERT: C 135 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: C 232 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9192 (mmtp) REVERT: B 161 VAL cc_start: 0.9173 (t) cc_final: 0.8911 (m) REVERT: A 62 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8412 (ttp-110) REVERT: A 143 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.4586 (mmm160) outliers start: 16 outliers final: 9 residues processed: 81 average time/residue: 0.6826 time to fit residues: 58.6517 Evaluate side-chains 72 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN B 306 GLN A 174 GLN D 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.057226 restraints weight = 22003.916| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.90 r_work: 0.2847 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10236 Z= 0.134 Angle : 0.435 6.040 13868 Z= 0.231 Chirality : 0.041 0.149 1540 Planarity : 0.003 0.042 1820 Dihedral : 7.809 63.580 1529 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.22 % Allowed : 13.20 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.25), residues: 1296 helix: 2.31 (0.22), residues: 572 sheet: 1.38 (0.34), residues: 304 loop : 0.41 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 62 TYR 0.011 0.001 TYR C 258 PHE 0.012 0.001 PHE C 240 TRP 0.005 0.001 TRP A 9 HIS 0.004 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00314 (10236) covalent geometry : angle 0.43500 (13868) hydrogen bonds : bond 0.03352 ( 478) hydrogen bonds : angle 4.39274 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.396 Fit side-chains REVERT: C 135 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: C 232 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9180 (mmtp) REVERT: B 161 VAL cc_start: 0.9189 (t) cc_final: 0.8913 (m) REVERT: A 62 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8424 (ttp-110) REVERT: A 143 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.4650 (mmm160) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.6417 time to fit residues: 51.0086 Evaluate side-chains 70 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 100 optimal weight: 0.0030 chunk 95 optimal weight: 0.3980 chunk 57 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN A 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059239 restraints weight = 21652.520| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.94 r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10236 Z= 0.092 Angle : 0.421 6.001 13868 Z= 0.224 Chirality : 0.040 0.144 1540 Planarity : 0.003 0.050 1820 Dihedral : 7.634 62.651 1529 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.22 % Allowed : 13.76 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.25), residues: 1296 helix: 2.36 (0.22), residues: 572 sheet: 1.44 (0.34), residues: 304 loop : 0.40 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 62 TYR 0.030 0.001 TYR B 258 PHE 0.010 0.001 PHE C 240 TRP 0.004 0.001 TRP A 9 HIS 0.003 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00211 (10236) covalent geometry : angle 0.42063 (13868) hydrogen bonds : bond 0.03037 ( 478) hydrogen bonds : angle 4.22069 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.292 Fit side-chains REVERT: C 85 ILE cc_start: 0.9433 (mt) cc_final: 0.9224 (mp) REVERT: C 135 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: C 161 VAL cc_start: 0.9207 (t) cc_final: 0.8833 (m) REVERT: B 161 VAL cc_start: 0.9173 (t) cc_final: 0.8903 (m) REVERT: A 62 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8436 (ttp-110) REVERT: A 143 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.4585 (mmm160) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.5471 time to fit residues: 47.8026 Evaluate side-chains 75 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN B 306 GLN A 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058628 restraints weight = 21686.094| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.87 r_work: 0.2879 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10236 Z= 0.109 Angle : 0.438 6.417 13868 Z= 0.230 Chirality : 0.041 0.146 1540 Planarity : 0.004 0.054 1820 Dihedral : 7.576 62.697 1528 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.22 % Allowed : 14.04 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.31 (0.25), residues: 1296 helix: 2.42 (0.22), residues: 572 sheet: 1.41 (0.34), residues: 304 loop : 0.44 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 62 TYR 0.030 0.001 TYR D 258 PHE 0.011 0.001 PHE C 240 TRP 0.004 0.001 TRP A 9 HIS 0.003 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00255 (10236) covalent geometry : angle 0.43774 (13868) hydrogen bonds : bond 0.03096 ( 478) hydrogen bonds : angle 4.30791 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.246 Fit side-chains REVERT: C 85 ILE cc_start: 0.9455 (mt) cc_final: 0.9248 (mp) REVERT: C 135 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: C 161 VAL cc_start: 0.9217 (t) cc_final: 0.8831 (m) REVERT: C 232 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9175 (mmtp) REVERT: B 161 VAL cc_start: 0.9183 (t) cc_final: 0.8912 (m) REVERT: A 62 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8451 (ttp-110) REVERT: A 143 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.4595 (mmm160) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.6408 time to fit residues: 52.9610 Evaluate side-chains 73 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 0.0030 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.073573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058940 restraints weight = 21546.901| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.89 r_work: 0.2888 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10236 Z= 0.102 Angle : 0.440 7.263 13868 Z= 0.233 Chirality : 0.041 0.146 1540 Planarity : 0.004 0.056 1820 Dihedral : 7.498 62.479 1528 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.03 % Allowed : 14.23 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.25), residues: 1296 helix: 2.45 (0.22), residues: 572 sheet: 1.42 (0.34), residues: 304 loop : 0.45 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 62 TYR 0.029 0.001 TYR B 258 PHE 0.011 0.001 PHE C 240 TRP 0.004 0.001 TRP A 9 HIS 0.003 0.000 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00237 (10236) covalent geometry : angle 0.44040 (13868) hydrogen bonds : bond 0.03025 ( 478) hydrogen bonds : angle 4.27451 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.296 Fit side-chains REVERT: C 85 ILE cc_start: 0.9448 (mt) cc_final: 0.9240 (mp) REVERT: C 135 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: C 161 VAL cc_start: 0.9212 (t) cc_final: 0.8812 (m) REVERT: C 232 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9177 (mmtp) REVERT: B 161 VAL cc_start: 0.9186 (t) cc_final: 0.8905 (m) REVERT: A 62 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8460 (ttp-110) REVERT: A 143 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.4626 (mmm160) REVERT: D 161 VAL cc_start: 0.9198 (t) cc_final: 0.8967 (m) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.7073 time to fit residues: 56.8461 Evaluate side-chains 70 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN B 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.071884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.057188 restraints weight = 21773.219| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.90 r_work: 0.2853 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10236 Z= 0.153 Angle : 0.471 6.933 13868 Z= 0.248 Chirality : 0.042 0.151 1540 Planarity : 0.003 0.059 1820 Dihedral : 7.624 62.905 1528 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.75 % Allowed : 14.61 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.25), residues: 1296 helix: 2.36 (0.22), residues: 572 sheet: 1.34 (0.34), residues: 304 loop : 0.52 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 62 TYR 0.012 0.001 TYR C 258 PHE 0.013 0.001 PHE C 240 TRP 0.005 0.001 TRP D 9 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00360 (10236) covalent geometry : angle 0.47050 (13868) hydrogen bonds : bond 0.03327 ( 478) hydrogen bonds : angle 4.41231 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.262 Fit side-chains REVERT: C 135 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 62 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8190 (ptm160) REVERT: A 143 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.4642 (mmm160) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.6782 time to fit residues: 49.4913 Evaluate side-chains 66 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.070549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055775 restraints weight = 22029.203| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.90 r_work: 0.2814 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10236 Z= 0.193 Angle : 0.501 7.491 13868 Z= 0.264 Chirality : 0.043 0.153 1540 Planarity : 0.003 0.058 1820 Dihedral : 7.866 63.289 1528 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.84 % Allowed : 14.51 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.25), residues: 1296 helix: 2.21 (0.22), residues: 572 sheet: 1.33 (0.34), residues: 304 loop : 0.47 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 62 TYR 0.028 0.002 TYR B 258 PHE 0.014 0.001 PHE C 240 TRP 0.007 0.001 TRP D 9 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00450 (10236) covalent geometry : angle 0.50135 (13868) hydrogen bonds : bond 0.03550 ( 478) hydrogen bonds : angle 4.57103 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.18 seconds wall clock time: 40 minutes 59.63 seconds (2459.63 seconds total)