Starting phenix.real_space_refine on Thu Feb 5 16:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818.map" model { file = "/net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2v_51818/02_2026/9h2v_51818_trim.cif" } resolution = 2.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 11823 2.51 5 N 3045 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s 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: 18032 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "C" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "D" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "E" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "F" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "G" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2540 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 6, 'TRANS': 317} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'D12': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'D12': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.60, per 1000 atoms: 0.26 Number of scatterers: 18032 At special positions: 0 Unit cell: (117.304, 118.25, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3108 8.00 N 3045 7.00 C 11823 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: 1.71 Conformation dependent library (CDL) restraints added in 816.7 milliseconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 58.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 Processing helix chain 'A' and resid 40 through 68 Processing helix chain 'A' and resid 76 through 107 Processing helix chain 'A' and resid 111 through 135 removed outlier: 3.805A pdb=" N ALA A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 Processing helix chain 'B' and resid 9 through 33 Processing helix chain 'B' and resid 40 through 68 Processing helix chain 'B' and resid 76 through 107 Processing helix chain 'B' and resid 111 through 135 removed outlier: 3.804A pdb=" N ALA B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 216 through 222 Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 314 Processing helix chain 'C' and resid 9 through 33 Processing helix chain 'C' and resid 40 through 68 Processing helix chain 'C' and resid 76 through 107 Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.805A pdb=" N ALA C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 314 Processing helix chain 'D' and resid 9 through 33 Processing helix chain 'D' and resid 40 through 68 Processing helix chain 'D' and resid 76 through 107 Processing helix chain 'D' and resid 111 through 135 removed outlier: 3.805A pdb=" N ALA D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 216 through 222 Processing helix chain 'D' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 314 Processing helix chain 'E' and resid 9 through 33 Processing helix chain 'E' and resid 40 through 68 Processing helix chain 'E' and resid 76 through 107 Processing helix chain 'E' and resid 111 through 135 removed outlier: 3.805A pdb=" N ALA E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 314 Processing helix chain 'F' and resid 9 through 33 Processing helix chain 'F' and resid 40 through 68 Processing helix chain 'F' and resid 76 through 107 Processing helix chain 'F' and resid 111 through 135 removed outlier: 3.806A pdb=" N ALA F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 314 Processing helix chain 'G' and resid 9 through 33 Processing helix chain 'G' and resid 40 through 68 Processing helix chain 'G' and resid 76 through 107 Processing helix chain 'G' and resid 111 through 135 removed outlier: 3.805A pdb=" N ALA G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 160 removed outlier: 5.262A pdb=" N VAL G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 216 through 222 Processing helix chain 'G' and resid 246 through 261 removed outlier: 3.617A pdb=" N GLU G 261 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 7.030A pdb=" N THR A 203 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL A 197 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR G 203 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL G 197 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR F 203 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL F 197 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER F 201 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR E 203 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL E 197 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR D 203 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL D 197 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR C 203 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL C 197 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B 203 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL B 197 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN A 283 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 326 removed outlier: 8.061A pdb=" N MET B 322 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP A 323 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 324 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN A 325 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE B 326 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N MET C 322 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 323 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL C 324 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 325 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE C 326 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N MET D 322 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP C 323 " --> pdb=" O MET D 322 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 324 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN C 325 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE D 326 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N MET E 322 " --> pdb=" O GLN D 321 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP D 323 " --> pdb=" O MET E 322 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 324 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN D 325 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE E 326 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N MET F 322 " --> pdb=" O GLN E 321 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP E 323 " --> pdb=" O MET F 322 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 324 " --> pdb=" O ASP E 323 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN E 325 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE F 326 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N MET G 322 " --> pdb=" O GLN F 321 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP F 323 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL G 324 " --> pdb=" O ASP F 323 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN F 325 " --> pdb=" O VAL G 324 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE G 326 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN B 283 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN C 283 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN D 283 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN E 283 " --> pdb=" O ASN E 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 232 through 241 removed outlier: 7.166A pdb=" N ASN F 283 " --> pdb=" O ASN F 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 232 through 241 removed outlier: 7.167A pdb=" N ASN G 283 " --> pdb=" O ASN G 275 " (cutoff:3.500A) 1263 hydrogen bonds defined for protein. 3705 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: 3.62 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5733 1.34 - 1.46: 3783 1.46 - 1.58: 8691 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18305 Sorted by residual: bond pdb=" CB PRO B 318 " pdb=" CG PRO B 318 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.10e-01 bond pdb=" CB PRO G 318 " pdb=" CG PRO G 318 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.08e-01 bond pdb=" CB PRO D 318 " pdb=" CG PRO D 318 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.02e-01 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.98e-01 bond pdb=" CB PRO E 318 " pdb=" CG PRO E 318 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.97e-01 ... (remaining 18300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 23724 0.87 - 1.73: 700 1.73 - 2.60: 153 2.60 - 3.47: 77 3.47 - 4.33: 14 Bond angle restraints: 24668 Sorted by residual: angle pdb=" N GLY D 39 " pdb=" CA GLY D 39 " pdb=" C GLY D 39 " ideal model delta sigma weight residual 114.67 110.34 4.33 1.10e+00 8.26e-01 1.55e+01 angle pdb=" N GLY G 39 " pdb=" CA GLY G 39 " pdb=" C GLY G 39 " ideal model delta sigma weight residual 114.67 110.34 4.33 1.10e+00 8.26e-01 1.55e+01 angle pdb=" N GLY C 39 " pdb=" CA GLY C 39 " pdb=" C GLY C 39 " ideal model delta sigma weight residual 114.67 110.35 4.32 1.10e+00 8.26e-01 1.54e+01 angle pdb=" N GLY A 39 " pdb=" CA GLY A 39 " pdb=" C GLY A 39 " ideal model delta sigma weight residual 114.67 110.37 4.30 1.10e+00 8.26e-01 1.53e+01 angle pdb=" N GLY F 39 " pdb=" CA GLY F 39 " pdb=" C GLY F 39 " ideal model delta sigma weight residual 114.67 110.37 4.30 1.10e+00 8.26e-01 1.53e+01 ... (remaining 24663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 9891 16.83 - 33.66: 749 33.66 - 50.48: 238 50.48 - 67.31: 56 67.31 - 84.14: 14 Dihedral angle restraints: 10948 sinusoidal: 4431 harmonic: 6517 Sorted by residual: dihedral pdb=" CA ALA G 107 " pdb=" C ALA G 107 " pdb=" N LYS G 108 " pdb=" CA LYS G 108 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA B 107 " pdb=" C ALA B 107 " pdb=" N LYS B 108 " pdb=" CA LYS B 108 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA D 107 " pdb=" C ALA D 107 " pdb=" N LYS D 108 " pdb=" CA LYS D 108 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 10945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1785 0.024 - 0.048: 621 0.048 - 0.073: 356 0.073 - 0.097: 52 0.097 - 0.121: 119 Chirality restraints: 2933 Sorted by residual: chirality pdb=" CA ILE B 282 " pdb=" N ILE B 282 " pdb=" C ILE B 282 " pdb=" CB ILE B 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE A 282 " pdb=" N ILE A 282 " pdb=" C ILE A 282 " pdb=" CB ILE A 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE D 282 " pdb=" N ILE D 282 " pdb=" C ILE D 282 " pdb=" CB ILE D 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 2930 not shown) Planarity restraints: 3059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 120 " -0.003 2.00e-02 2.50e+03 6.29e-03 3.96e-01 pdb=" C ARG C 120 " 0.011 2.00e-02 2.50e+03 pdb=" O ARG C 120 " -0.004 2.00e-02 2.50e+03 pdb=" N ILE C 121 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 120 " -0.003 2.00e-02 2.50e+03 6.18e-03 3.82e-01 pdb=" C ARG G 120 " 0.011 2.00e-02 2.50e+03 pdb=" O ARG G 120 " -0.004 2.00e-02 2.50e+03 pdb=" N ILE G 121 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 120 " 0.003 2.00e-02 2.50e+03 6.17e-03 3.81e-01 pdb=" C ARG D 120 " -0.011 2.00e-02 2.50e+03 pdb=" O ARG D 120 " 0.004 2.00e-02 2.50e+03 pdb=" N ILE D 121 " 0.004 2.00e-02 2.50e+03 ... (remaining 3056 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 6569 2.87 - 3.38: 18968 3.38 - 3.88: 29560 3.88 - 4.39: 33013 4.39 - 4.90: 57117 Nonbonded interactions: 145227 Sorted by model distance: nonbonded pdb=" O ASP C 323 " pdb=" N MET D 322 " model vdw 2.358 3.120 nonbonded pdb=" N ASP E 111 " pdb=" OD1 ASP E 111 " model vdw 2.378 3.120 nonbonded pdb=" N ASP C 111 " pdb=" OD1 ASP C 111 " model vdw 2.378 3.120 nonbonded pdb=" N ASP G 111 " pdb=" OD1 ASP G 111 " model vdw 2.378 3.120 nonbonded pdb=" N ASP A 111 " pdb=" OD1 ASP A 111 " model vdw 2.378 3.120 ... (remaining 145222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 402) selection = (chain 'B' and resid 6 through 402) selection = (chain 'C' and resid 6 through 402) selection = (chain 'D' and resid 6 through 402) selection = (chain 'E' and resid 6 through 402) selection = (chain 'F' and resid 6 through 402) selection = chain 'G' } 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: 1.230 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.380 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 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 : 0.002 0.039 18305 Z= 0.106 Angle : 0.401 4.333 24668 Z= 0.246 Chirality : 0.037 0.121 2933 Planarity : 0.001 0.010 3059 Dihedral : 14.023 84.141 6748 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.14 % Allowed : 19.22 % Favored : 79.64 % 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: 3.01 (0.19), residues: 2254 helix: 3.81 (0.14), residues: 1281 sheet: 0.22 (0.33), residues: 280 loop : -0.95 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 177 TYR 0.006 0.001 TYR B 319 PHE 0.006 0.001 PHE B 30 TRP 0.004 0.000 TRP F 29 HIS 0.002 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00221 (18305) covalent geometry : angle 0.40098 (24668) hydrogen bonds : bond 0.14960 ( 1263) hydrogen bonds : angle 5.41605 ( 3705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.672 Fit side-chains REVERT: C 26 MET cc_start: 0.5893 (ttp) cc_final: 0.5671 (ttt) REVERT: C 198 GLN cc_start: 0.7231 (mt0) cc_final: 0.6864 (mm-40) REVERT: C 236 GLU cc_start: 0.9138 (tt0) cc_final: 0.8888 (tt0) REVERT: D 236 GLU cc_start: 0.9141 (tt0) cc_final: 0.8939 (tt0) REVERT: E 165 SER cc_start: 0.7244 (m) cc_final: 0.6876 (p) REVERT: E 236 GLU cc_start: 0.9210 (tt0) cc_final: 0.8987 (tt0) REVERT: F 236 GLU cc_start: 0.9156 (tt0) cc_final: 0.8906 (tt0) REVERT: G 236 GLU cc_start: 0.9094 (tt0) cc_final: 0.8880 (tt0) outliers start: 22 outliers final: 1 residues processed: 215 average time/residue: 0.5461 time to fit residues: 133.6619 Evaluate side-chains 161 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 321 GLN C 321 GLN D 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.210867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120565 restraints weight = 19191.319| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.42 r_work: 0.3272 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18305 Z= 0.214 Angle : 0.604 11.818 24668 Z= 0.315 Chirality : 0.046 0.174 2933 Planarity : 0.003 0.032 3059 Dihedral : 6.335 59.812 2648 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.42 % Allowed : 17.45 % Favored : 78.13 % 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: 2.11 (0.18), residues: 2254 helix: 3.00 (0.14), residues: 1274 sheet: -0.08 (0.30), residues: 294 loop : -1.13 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 268 TYR 0.016 0.002 TYR D 319 PHE 0.014 0.002 PHE D 42 TRP 0.004 0.001 TRP G 29 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00517 (18305) covalent geometry : angle 0.60390 (24668) hydrogen bonds : bond 0.04577 ( 1263) hydrogen bonds : angle 4.00621 ( 3705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 145 time to evaluate : 0.696 Fit side-chains REVERT: A 309 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7182 (mm-30) REVERT: B 256 ASN cc_start: 0.6459 (m-40) cc_final: 0.6119 (m-40) REVERT: C 26 MET cc_start: 0.6220 (ttp) cc_final: 0.6005 (ttt) REVERT: D 180 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6882 (mtt90) REVERT: E 177 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6839 (mtm180) REVERT: E 230 GLU cc_start: 0.8456 (tp30) cc_final: 0.8164 (mm-30) outliers start: 85 outliers final: 16 residues processed: 191 average time/residue: 0.6247 time to fit residues: 133.9456 Evaluate side-chains 131 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN C 283 ASN D 325 ASN E 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.212641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122713 restraints weight = 19386.300| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.44 r_work: 0.3285 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18305 Z= 0.127 Angle : 0.489 8.655 24668 Z= 0.255 Chirality : 0.042 0.180 2933 Planarity : 0.002 0.022 3059 Dihedral : 5.626 58.943 2646 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.13 % Allowed : 18.86 % Favored : 79.01 % 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: 2.00 (0.18), residues: 2254 helix: 2.78 (0.14), residues: 1316 sheet: -0.23 (0.28), residues: 294 loop : -1.09 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 177 TYR 0.006 0.001 TYR D 319 PHE 0.013 0.001 PHE A 237 TRP 0.002 0.000 TRP E 300 HIS 0.002 0.001 HIS E 43 Details of bonding type rmsd covalent geometry : bond 0.00293 (18305) covalent geometry : angle 0.48937 (24668) hydrogen bonds : bond 0.03757 ( 1263) hydrogen bonds : angle 3.66934 ( 3705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.733 Fit side-chains REVERT: A 309 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7189 (mm-30) REVERT: D 26 MET cc_start: 0.5235 (tmt) cc_final: 0.4976 (tmm) REVERT: D 259 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7183 (mm-40) REVERT: E 177 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6997 (mtm180) REVERT: E 230 GLU cc_start: 0.8602 (tp30) cc_final: 0.8317 (mm-30) REVERT: E 259 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7172 (mm110) outliers start: 41 outliers final: 10 residues processed: 142 average time/residue: 0.6465 time to fit residues: 103.1388 Evaluate side-chains 121 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 177 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 98 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 32 optimal weight: 50.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 GLN D 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.212443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122594 restraints weight = 19307.213| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.45 r_work: 0.3290 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18305 Z= 0.119 Angle : 0.483 7.686 24668 Z= 0.251 Chirality : 0.041 0.206 2933 Planarity : 0.002 0.018 3059 Dihedral : 5.238 59.567 2646 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.18 % Allowed : 18.39 % Favored : 79.43 % 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: 2.00 (0.17), residues: 2254 helix: 2.74 (0.14), residues: 1316 sheet: -0.24 (0.27), residues: 294 loop : -0.97 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 233 TYR 0.007 0.001 TYR G 50 PHE 0.015 0.001 PHE G 42 TRP 0.004 0.000 TRP B 29 HIS 0.003 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00272 (18305) covalent geometry : angle 0.48348 (24668) hydrogen bonds : bond 0.03540 ( 1263) hydrogen bonds : angle 3.54914 ( 3705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.706 Fit side-chains REVERT: D 26 MET cc_start: 0.5395 (tmt) cc_final: 0.5133 (tmm) REVERT: D 259 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7090 (mm-40) REVERT: E 230 GLU cc_start: 0.8533 (tp30) cc_final: 0.8267 (mm-30) REVERT: E 259 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7075 (mm110) REVERT: G 309 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7109 (mm-30) outliers start: 42 outliers final: 13 residues processed: 146 average time/residue: 0.6225 time to fit residues: 102.3792 Evaluate side-chains 120 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 212 optimal weight: 0.0070 chunk 7 optimal weight: 30.0000 chunk 219 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.211976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122216 restraints weight = 19007.693| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.45 r_work: 0.3238 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18305 Z= 0.196 Angle : 0.531 7.375 24668 Z= 0.277 Chirality : 0.043 0.202 2933 Planarity : 0.003 0.028 3059 Dihedral : 5.352 56.917 2646 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.65 % Allowed : 18.44 % Favored : 78.91 % 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: 1.80 (0.17), residues: 2254 helix: 2.58 (0.14), residues: 1316 sheet: -0.07 (0.26), residues: 294 loop : -1.19 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 233 TYR 0.012 0.001 TYR D 319 PHE 0.017 0.001 PHE D 237 TRP 0.005 0.001 TRP F 29 HIS 0.002 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00481 (18305) covalent geometry : angle 0.53051 (24668) hydrogen bonds : bond 0.03985 ( 1263) hydrogen bonds : angle 3.70866 ( 3705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.705 Fit side-chains REVERT: B 26 MET cc_start: 0.7573 (tpp) cc_final: 0.6970 (tmm) REVERT: C 177 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7410 (mtp-110) REVERT: D 26 MET cc_start: 0.5795 (tmt) cc_final: 0.5541 (tmm) REVERT: D 180 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6617 (mtt90) REVERT: E 326 PHE cc_start: 0.8301 (m-10) cc_final: 0.7723 (m-80) REVERT: F 177 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7548 (ttp-110) REVERT: G 26 MET cc_start: 0.7052 (tmm) cc_final: 0.6504 (tmm) REVERT: G 177 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7300 (mtp-110) REVERT: G 180 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6901 (mtt90) outliers start: 51 outliers final: 18 residues processed: 156 average time/residue: 0.6560 time to fit residues: 114.6461 Evaluate side-chains 141 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 133 optimal weight: 40.0000 chunk 218 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 217 optimal weight: 0.0030 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.211673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122526 restraints weight = 19119.092| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.45 r_work: 0.3284 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18305 Z= 0.107 Angle : 0.464 6.603 24668 Z= 0.239 Chirality : 0.041 0.219 2933 Planarity : 0.002 0.019 3059 Dihedral : 4.982 58.815 2646 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.66 % Allowed : 19.64 % Favored : 78.70 % 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: 2.04 (0.17), residues: 2254 helix: 2.74 (0.14), residues: 1316 sheet: -0.08 (0.27), residues: 280 loop : -0.95 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 268 TYR 0.005 0.001 TYR C 134 PHE 0.015 0.001 PHE C 42 TRP 0.002 0.000 TRP G 289 HIS 0.003 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00241 (18305) covalent geometry : angle 0.46444 (24668) hydrogen bonds : bond 0.03317 ( 1263) hydrogen bonds : angle 3.48495 ( 3705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.671 Fit side-chains REVERT: B 26 MET cc_start: 0.7671 (tpp) cc_final: 0.7115 (tmm) REVERT: D 26 MET cc_start: 0.5886 (tmt) cc_final: 0.5656 (tmm) REVERT: D 180 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6625 (mtt90) REVERT: D 259 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7091 (mm-40) REVERT: E 230 GLU cc_start: 0.8619 (tp30) cc_final: 0.8271 (mm-30) REVERT: E 259 GLN cc_start: 0.7415 (mm-40) cc_final: 0.7080 (mm110) REVERT: G 26 MET cc_start: 0.7094 (tmm) cc_final: 0.6767 (tmm) REVERT: G 259 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6789 (mm110) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.6183 time to fit residues: 107.5806 Evaluate side-chains 142 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 139 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 128 optimal weight: 40.0000 chunk 33 optimal weight: 40.0000 chunk 56 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 192 optimal weight: 30.0000 chunk 219 optimal weight: 0.5980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.208698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119175 restraints weight = 19287.457| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.52 r_work: 0.3236 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18305 Z= 0.162 Angle : 0.509 9.493 24668 Z= 0.262 Chirality : 0.042 0.234 2933 Planarity : 0.003 0.024 3059 Dihedral : 5.122 57.685 2646 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.92 % Allowed : 19.95 % Favored : 78.13 % 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: 1.95 (0.17), residues: 2254 helix: 2.65 (0.14), residues: 1316 sheet: -0.11 (0.27), residues: 280 loop : -0.95 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 233 TYR 0.019 0.001 TYR F 50 PHE 0.015 0.001 PHE G 237 TRP 0.005 0.001 TRP F 29 HIS 0.002 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00393 (18305) covalent geometry : angle 0.50888 (24668) hydrogen bonds : bond 0.03683 ( 1263) hydrogen bonds : angle 3.59869 ( 3705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.702 Fit side-chains REVERT: B 26 MET cc_start: 0.7624 (tpp) cc_final: 0.7023 (tmm) REVERT: D 26 MET cc_start: 0.6130 (tmt) cc_final: 0.5925 (tmm) REVERT: D 180 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6649 (mtt90) REVERT: E 326 PHE cc_start: 0.8308 (m-10) cc_final: 0.7710 (m-80) REVERT: G 26 MET cc_start: 0.7149 (tmm) cc_final: 0.6779 (tmm) outliers start: 37 outliers final: 21 residues processed: 143 average time/residue: 0.6114 time to fit residues: 98.4681 Evaluate side-chains 144 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 199 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 chunk 73 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.211822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122506 restraints weight = 18957.319| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.46 r_work: 0.3237 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18305 Z= 0.168 Angle : 0.501 9.048 24668 Z= 0.258 Chirality : 0.042 0.243 2933 Planarity : 0.003 0.024 3059 Dihedral : 5.022 55.519 2646 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 20.10 % Favored : 77.82 % 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: 1.94 (0.17), residues: 2254 helix: 2.63 (0.14), residues: 1316 sheet: -0.06 (0.26), residues: 294 loop : -0.97 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 268 TYR 0.010 0.001 TYR F 50 PHE 0.015 0.001 PHE C 42 TRP 0.005 0.001 TRP F 29 HIS 0.001 0.000 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00411 (18305) covalent geometry : angle 0.50124 (24668) hydrogen bonds : bond 0.03578 ( 1263) hydrogen bonds : angle 3.56673 ( 3705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.457 Fit side-chains REVERT: B 26 MET cc_start: 0.7697 (tpp) cc_final: 0.7080 (tmm) REVERT: C 26 MET cc_start: 0.7309 (tmm) cc_final: 0.7061 (ttt) REVERT: D 180 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6647 (mtt90) REVERT: E 326 PHE cc_start: 0.8270 (m-10) cc_final: 0.7648 (m-80) REVERT: G 26 MET cc_start: 0.7321 (tmm) cc_final: 0.7038 (tmm) REVERT: G 180 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6878 (mtt90) outliers start: 40 outliers final: 19 residues processed: 163 average time/residue: 0.4943 time to fit residues: 91.6732 Evaluate side-chains 149 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 206 optimal weight: 8.9990 chunk 180 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.211934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123371 restraints weight = 18870.773| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.45 r_work: 0.3252 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18305 Z= 0.145 Angle : 0.507 9.650 24668 Z= 0.255 Chirality : 0.042 0.242 2933 Planarity : 0.003 0.025 3059 Dihedral : 5.002 54.677 2646 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 21.19 % Favored : 77.45 % 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: 2.00 (0.17), residues: 2254 helix: 2.67 (0.14), residues: 1316 sheet: -0.08 (0.26), residues: 294 loop : -0.92 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 116 TYR 0.014 0.001 TYR F 50 PHE 0.014 0.001 PHE G 237 TRP 0.004 0.000 TRP F 29 HIS 0.001 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00350 (18305) covalent geometry : angle 0.50666 (24668) hydrogen bonds : bond 0.03472 ( 1263) hydrogen bonds : angle 3.53709 ( 3705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.552 Fit side-chains REVERT: A 26 MET cc_start: 0.8130 (tpt) cc_final: 0.7245 (tmm) REVERT: B 26 MET cc_start: 0.7760 (tpp) cc_final: 0.7155 (tmm) REVERT: D 180 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6588 (mtt90) REVERT: E 26 MET cc_start: 0.4962 (ttp) cc_final: 0.4639 (ttt) REVERT: G 26 MET cc_start: 0.7372 (tmm) cc_final: 0.7120 (tmm) REVERT: G 180 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6781 (mtt90) outliers start: 26 outliers final: 17 residues processed: 143 average time/residue: 0.5023 time to fit residues: 81.6425 Evaluate side-chains 150 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 130 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 194 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.210519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122538 restraints weight = 19105.043| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.45 r_work: 0.3287 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18305 Z= 0.099 Angle : 0.491 9.954 24668 Z= 0.244 Chirality : 0.041 0.243 2933 Planarity : 0.002 0.028 3059 Dihedral : 4.815 54.171 2646 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.99 % Allowed : 21.71 % Favored : 77.30 % 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: 2.16 (0.17), residues: 2254 helix: 2.78 (0.14), residues: 1316 sheet: -0.05 (0.27), residues: 280 loop : -0.74 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 116 TYR 0.032 0.001 TYR F 50 PHE 0.015 0.001 PHE B 95 TRP 0.002 0.000 TRP G 300 HIS 0.001 0.000 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00222 (18305) covalent geometry : angle 0.49137 (24668) hydrogen bonds : bond 0.03165 ( 1263) hydrogen bonds : angle 3.43881 ( 3705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.708 Fit side-chains REVERT: A 26 MET cc_start: 0.8214 (tpt) cc_final: 0.7289 (tmm) REVERT: B 26 MET cc_start: 0.7751 (tpp) cc_final: 0.7151 (tmm) REVERT: C 26 MET cc_start: 0.7601 (tpt) cc_final: 0.6906 (tmm) REVERT: D 180 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6607 (mtt90) REVERT: E 26 MET cc_start: 0.5049 (ttp) cc_final: 0.4765 (ttt) REVERT: E 230 GLU cc_start: 0.8534 (tp30) cc_final: 0.8157 (mm-30) REVERT: G 26 MET cc_start: 0.7372 (tmm) cc_final: 0.7113 (tmm) REVERT: G 180 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6882 (mtt90) outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 0.6016 time to fit residues: 98.0910 Evaluate side-chains 144 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 177 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 16 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 91 optimal weight: 0.1980 chunk 180 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4383 r_free = 0.4383 target = 0.208079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120068 restraints weight = 19193.654| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.45 r_work: 0.3249 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18305 Z= 0.140 Angle : 0.514 9.744 24668 Z= 0.257 Chirality : 0.042 0.246 2933 Planarity : 0.003 0.029 3059 Dihedral : 4.906 57.484 2646 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 21.40 % Favored : 77.19 % 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: 2.12 (0.17), residues: 2254 helix: 2.74 (0.14), residues: 1316 sheet: -0.06 (0.26), residues: 294 loop : -0.77 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 116 TYR 0.027 0.001 TYR F 50 PHE 0.017 0.001 PHE A 95 TRP 0.004 0.000 TRP C 29 HIS 0.001 0.000 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00338 (18305) covalent geometry : angle 0.51407 (24668) hydrogen bonds : bond 0.03408 ( 1263) hydrogen bonds : angle 3.51089 ( 3705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7828.32 seconds wall clock time: 133 minutes 46.90 seconds (8026.90 seconds total)