Starting phenix.real_space_refine on Sun Aug 24 16:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3p_17389/08_2025/8p3p_17389.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 120 5.16 5 C 13408 2.51 5 N 3776 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21224 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "A" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "D" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2653 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 5.51, per 1000 atoms: 0.26 Number of scatterers: 21224 At special positions: 0 Unit cell: (123.372, 123.372, 169.74, 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 120 16.00 O 3920 8.00 N 3776 7.00 C 13408 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: 1.93 Conformation dependent library (CDL) restraints added in 918.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 70.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'C' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.673A pdb=" N GLY C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 95 through 109 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.679A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.687A pdb=" N ARG C 155 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 238 Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.628A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 50 removed outlier: 3.510A pdb=" N ILE H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 70 removed outlier: 3.801A pdb=" N GLY H 70 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 121 through 127 removed outlier: 3.699A pdb=" N ARG H 127 " --> pdb=" O TYR H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.673A pdb=" N MET H 256 " --> pdb=" O ASP H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.613A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 348 Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.501A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.675A pdb=" N GLY A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.678A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.687A pdb=" N ARG A 155 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 238 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.627A pdb=" N ARG B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 removed outlier: 3.511A pdb=" N ILE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.812A pdb=" N GLY B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.700A pdb=" N ARG B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.677A pdb=" N MET B 256 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.613A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 348 Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.704A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.674A pdb=" N GLY D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 95 through 109 Processing helix chain 'D' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.677A pdb=" N ILE D 146 " --> pdb=" O MET D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.702A pdb=" N ARG D 155 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.628A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 50 removed outlier: 3.510A pdb=" N ILE E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.810A pdb=" N GLY E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.745A pdb=" N SER E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 121 through 127 removed outlier: 3.699A pdb=" N ARG E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 167 through 237 removed outlier: 3.563A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.675A pdb=" N MET E 256 " --> pdb=" O ASP E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.612A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 348 Processing helix chain 'F' and resid 18 through 24 removed outlier: 3.703A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 50 removed outlier: 3.502A pdb=" N ILE F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.673A pdb=" N GLY F 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 86 Processing helix chain 'F' and resid 95 through 109 Processing helix chain 'F' and resid 110 through 120 removed outlier: 3.685A pdb=" N GLN F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 146 removed outlier: 3.679A pdb=" N ILE F 146 " --> pdb=" O MET F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.688A pdb=" N ARG F 155 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 294 removed outlier: 3.737A pdb=" N VAL F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 346 removed outlier: 4.388A pdb=" N CYS F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.634A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 50 removed outlier: 3.509A pdb=" N ILE G 33 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.812A pdb=" N GLY G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.734A pdb=" N SER G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 121 through 127 removed outlier: 3.700A pdb=" N ARG G 127 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 167 through 237 removed outlier: 3.562A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.675A pdb=" N MET G 256 " --> pdb=" O ASP G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 275 Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.612A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 348 Processing sheet with id=AA1, first strand: chain 'C' and resid 147 through 149 removed outlier: 6.127A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 146 through 149 removed outlier: 6.583A pdb=" N ASP H 62 " --> pdb=" O TYR H 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR H 307 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.585A pdb=" N ASP B 62 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR B 307 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE D 60 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.584A pdb=" N ASP E 62 " --> pdb=" O TYR E 307 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR E 307 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 147 through 149 removed outlier: 6.128A pdb=" N ILE F 60 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 146 through 149 removed outlier: 6.584A pdb=" N ASP G 62 " --> pdb=" O TYR G 307 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR G 307 " --> pdb=" O ASP G 62 " (cutoff:3.500A) 1520 hydrogen bonds defined for protein. 4416 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: 3.71 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7180 1.35 - 1.46: 4896 1.46 - 1.58: 9340 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21648 Sorted by residual: bond pdb=" N MET G 328 " pdb=" CA MET G 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.92e+00 bond pdb=" N MET E 328 " pdb=" CA MET E 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.92e+00 bond pdb=" N MET H 328 " pdb=" CA MET H 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 bond pdb=" N MET B 328 " pdb=" CA MET B 328 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.84e+00 bond pdb=" CB GLU E 249 " pdb=" CG GLU E 249 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 28933 2.27 - 4.55: 255 4.55 - 6.82: 78 6.82 - 9.10: 14 9.10 - 11.37: 16 Bond angle restraints: 29296 Sorted by residual: angle pdb=" CB MET G 224 " pdb=" CG MET G 224 " pdb=" SD MET G 224 " ideal model delta sigma weight residual 112.70 124.07 -11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CB MET H 224 " pdb=" CG MET H 224 " pdb=" SD MET H 224 " ideal model delta sigma weight residual 112.70 124.07 -11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CB MET B 224 " pdb=" CG MET B 224 " pdb=" SD MET B 224 " ideal model delta sigma weight residual 112.70 124.06 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET E 224 " pdb=" CG MET E 224 " pdb=" SD MET E 224 " ideal model delta sigma weight residual 112.70 124.03 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET D 256 " pdb=" CG MET D 256 " pdb=" SD MET D 256 " ideal model delta sigma weight residual 112.70 123.01 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 29291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 11331 17.83 - 35.67: 1398 35.67 - 53.50: 358 53.50 - 71.34: 53 71.34 - 89.17: 12 Dihedral angle restraints: 13152 sinusoidal: 5376 harmonic: 7776 Sorted by residual: dihedral pdb=" CA ASP C 92 " pdb=" CB ASP C 92 " pdb=" CG ASP C 92 " pdb=" OD1 ASP C 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.69 57.69 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP D 92 " pdb=" CB ASP D 92 " pdb=" CG ASP D 92 " pdb=" OD1 ASP D 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP F 92 " pdb=" CB ASP F 92 " pdb=" CG ASP F 92 " pdb=" OD1 ASP F 92 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 13149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1969 0.025 - 0.049: 740 0.049 - 0.074: 319 0.074 - 0.099: 110 0.099 - 0.124: 46 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CA ILE H 149 " pdb=" N ILE H 149 " pdb=" C ILE H 149 " pdb=" CB ILE H 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE E 149 " pdb=" N ILE E 149 " pdb=" C ILE E 149 " pdb=" CB ILE E 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA MET H 68 " pdb=" N MET H 68 " pdb=" C MET H 68 " pdb=" CB MET H 68 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 3181 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 249 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" CD GLU B 249 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 249 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 249 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 249 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" CD GLU E 249 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU E 249 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU E 249 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 249 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" CD GLU H 249 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU H 249 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU H 249 " 0.012 2.00e-02 2.50e+03 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5045 2.79 - 3.32: 21116 3.32 - 3.85: 36383 3.85 - 4.37: 39611 4.37 - 4.90: 70005 Nonbonded interactions: 172160 Sorted by model distance: nonbonded pdb=" O LEU C 108 " pdb=" OH TYR C 178 " model vdw 2.267 3.040 nonbonded pdb=" O LEU D 108 " pdb=" OH TYR D 178 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 108 " pdb=" OH TYR A 178 " model vdw 2.269 3.040 nonbonded pdb=" O LEU F 108 " pdb=" OH TYR F 178 " model vdw 2.269 3.040 nonbonded pdb=" O GLY G 71 " pdb=" OG SER G 74 " model vdw 2.339 3.040 ... (remaining 172155 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 10.260 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.210 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21648 Z= 0.134 Angle : 0.626 11.373 29296 Z= 0.300 Chirality : 0.035 0.124 3184 Planarity : 0.004 0.035 3840 Dihedral : 16.190 89.170 8112 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.86 % Allowed : 23.41 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.26 (0.17), residues: 2640 helix: 3.22 (0.12), residues: 1760 sheet: 2.41 (0.50), residues: 156 loop : -0.77 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 52 TYR 0.014 0.001 TYR C 123 PHE 0.027 0.001 PHE A 324 TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS F 237 Details of bonding type rmsd covalent geometry : bond 0.00288 (21648) covalent geometry : angle 0.62593 (29296) hydrogen bonds : bond 0.11442 ( 1520) hydrogen bonds : angle 4.33442 ( 4416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7350 (t0) cc_final: 0.7000 (t0) REVERT: A 152 ASP cc_start: 0.7346 (t0) cc_final: 0.6997 (t0) REVERT: D 155 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8529 (mpp80) REVERT: F 152 ASP cc_start: 0.7352 (t0) cc_final: 0.7003 (t0) outliers start: 19 outliers final: 12 residues processed: 204 average time/residue: 0.7946 time to fit residues: 180.1119 Evaluate side-chains 188 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 226 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.127456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.074199 restraints weight = 34949.067| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.88 r_work: 0.2789 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21648 Z= 0.142 Angle : 0.548 7.501 29296 Z= 0.270 Chirality : 0.036 0.153 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.857 36.325 2968 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.45 % Allowed : 21.51 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.63 (0.17), residues: 2640 helix: 3.51 (0.12), residues: 1776 sheet: 2.37 (0.49), residues: 156 loop : -0.72 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 155 TYR 0.016 0.001 TYR C 123 PHE 0.019 0.001 PHE D 324 TRP 0.011 0.001 TRP E 111 HIS 0.002 0.001 HIS H 237 Details of bonding type rmsd covalent geometry : bond 0.00317 (21648) covalent geometry : angle 0.54790 (29296) hydrogen bonds : bond 0.04306 ( 1520) hydrogen bonds : angle 3.25872 ( 4416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ASP cc_start: 0.7700 (t0) cc_final: 0.7480 (t0) REVERT: C 155 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8642 (mtm-85) REVERT: H 301 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7402 (mmp80) REVERT: A 152 ASP cc_start: 0.7693 (t0) cc_final: 0.7471 (t0) REVERT: A 155 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8636 (mtm-85) REVERT: B 301 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7401 (mmp80) REVERT: D 155 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8557 (mpp80) REVERT: E 301 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7402 (mmp80) REVERT: F 152 ASP cc_start: 0.7703 (t0) cc_final: 0.7484 (t0) REVERT: F 155 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8634 (mtm-85) REVERT: G 301 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7397 (mmp80) outliers start: 32 outliers final: 9 residues processed: 215 average time/residue: 0.8573 time to fit residues: 204.2040 Evaluate side-chains 197 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN E 87 ASN G 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073885 restraints weight = 35017.598| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.88 r_work: 0.2785 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21648 Z= 0.142 Angle : 0.538 7.700 29296 Z= 0.263 Chirality : 0.035 0.121 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.654 36.678 2958 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.81 % Allowed : 20.61 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.68 (0.17), residues: 2640 helix: 3.53 (0.12), residues: 1776 sheet: 2.33 (0.49), residues: 156 loop : -0.62 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 63 TYR 0.017 0.001 TYR C 123 PHE 0.012 0.001 PHE C 302 TRP 0.010 0.001 TRP E 111 HIS 0.001 0.000 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00321 (21648) covalent geometry : angle 0.53808 (29296) hydrogen bonds : bond 0.04180 ( 1520) hydrogen bonds : angle 3.15087 ( 4416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8665 (mtm-85) REVERT: H 63 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8178 (mtp-110) REVERT: H 301 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7486 (mmp80) REVERT: H 335 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 155 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8660 (mtm-85) REVERT: B 301 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7453 (mmp80) REVERT: B 335 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6653 (mp) REVERT: D 155 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8557 (mpp80) REVERT: E 63 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8177 (mtp-110) REVERT: E 301 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7455 (mmp80) REVERT: E 335 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6699 (mp) REVERT: F 155 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8666 (mtm-85) REVERT: G 63 ARG cc_start: 0.8366 (mtm110) cc_final: 0.8154 (mtp-110) REVERT: G 301 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7460 (mmp80) REVERT: G 335 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6708 (mp) outliers start: 62 outliers final: 15 residues processed: 230 average time/residue: 0.7932 time to fit residues: 203.4237 Evaluate side-chains 210 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 25 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 114 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 198 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN E 87 ASN G 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072959 restraints weight = 35088.066| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.96 r_work: 0.2786 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21648 Z= 0.139 Angle : 0.542 7.972 29296 Z= 0.263 Chirality : 0.035 0.157 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.642 36.774 2958 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.90 % Allowed : 21.11 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.69 (0.17), residues: 2640 helix: 3.54 (0.12), residues: 1776 sheet: 2.34 (0.49), residues: 156 loop : -0.63 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 85 TYR 0.016 0.001 TYR A 123 PHE 0.025 0.001 PHE C 324 TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00315 (21648) covalent geometry : angle 0.54176 (29296) hydrogen bonds : bond 0.04099 ( 1520) hydrogen bonds : angle 3.11511 ( 4416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8950 (mtm-85) cc_final: 0.8504 (mpp80) REVERT: H 301 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7450 (mmp80) REVERT: A 155 ARG cc_start: 0.8949 (mtm-85) cc_final: 0.8503 (mpp80) REVERT: B 301 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7445 (mmp80) REVERT: B 335 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6694 (mp) REVERT: D 155 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8636 (mpp80) REVERT: E 301 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7449 (mmp80) REVERT: F 155 ARG cc_start: 0.8949 (mtm-85) cc_final: 0.8503 (mpp80) REVERT: G 301 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7447 (mmp80) outliers start: 64 outliers final: 22 residues processed: 221 average time/residue: 0.7720 time to fit residues: 191.0180 Evaluate side-chains 213 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 94 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 263 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN E 87 ASN G 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070984 restraints weight = 34957.279| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.98 r_work: 0.2746 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21648 Z= 0.206 Angle : 0.582 8.362 29296 Z= 0.284 Chirality : 0.037 0.120 3184 Planarity : 0.003 0.033 3840 Dihedral : 3.805 38.462 2958 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.17 % Allowed : 20.70 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.59 (0.17), residues: 2640 helix: 3.46 (0.12), residues: 1780 sheet: 2.09 (0.48), residues: 160 loop : -0.65 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.019 0.002 TYR A 123 PHE 0.015 0.001 PHE A 302 TRP 0.008 0.001 TRP E 111 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00487 (21648) covalent geometry : angle 0.58152 (29296) hydrogen bonds : bond 0.04636 ( 1520) hydrogen bonds : angle 3.17280 ( 4416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8521 (mpp80) REVERT: H 301 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (mmp80) REVERT: H 335 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6705 (mp) REVERT: A 155 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8530 (mpp80) REVERT: B 301 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: B 335 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6641 (mp) REVERT: D 155 ARG cc_start: 0.9002 (mtm-85) cc_final: 0.8624 (mpp80) REVERT: E 301 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7522 (mmp80) REVERT: E 335 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6706 (mp) REVERT: F 155 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8527 (mpp80) REVERT: G 301 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7523 (mmp80) REVERT: G 335 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6675 (mp) outliers start: 70 outliers final: 15 residues processed: 227 average time/residue: 0.7978 time to fit residues: 201.5704 Evaluate side-chains 201 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 187 optimal weight: 0.0870 chunk 186 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 221 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.127836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073494 restraints weight = 34862.563| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.92 r_work: 0.2804 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21648 Z= 0.121 Angle : 0.565 9.372 29296 Z= 0.268 Chirality : 0.035 0.124 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.668 38.462 2958 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 22.33 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.74 (0.17), residues: 2640 helix: 3.60 (0.12), residues: 1776 sheet: 2.34 (0.50), residues: 156 loop : -0.67 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 63 TYR 0.015 0.001 TYR D 123 PHE 0.026 0.001 PHE D 324 TRP 0.009 0.001 TRP E 111 HIS 0.000 0.000 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00264 (21648) covalent geometry : angle 0.56480 (29296) hydrogen bonds : bond 0.03867 ( 1520) hydrogen bonds : angle 3.07261 ( 4416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8562 (mpp80) REVERT: H 301 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7434 (mmp80) REVERT: H 335 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6709 (mp) REVERT: A 155 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8559 (mpp80) REVERT: B 301 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7446 (mmp80) REVERT: D 155 ARG cc_start: 0.9038 (mtm-85) cc_final: 0.8559 (mpp80) REVERT: E 301 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7438 (mmp80) REVERT: E 335 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6709 (mp) REVERT: F 155 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8563 (mpp80) REVERT: G 301 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7456 (mmp80) REVERT: G 335 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6700 (mp) outliers start: 47 outliers final: 12 residues processed: 205 average time/residue: 0.7763 time to fit residues: 177.5732 Evaluate side-chains 203 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN B 87 ASN E 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.127406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072678 restraints weight = 34952.083| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.97 r_work: 0.2785 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21648 Z= 0.142 Angle : 0.591 9.266 29296 Z= 0.278 Chirality : 0.036 0.122 3184 Planarity : 0.003 0.035 3840 Dihedral : 3.681 38.786 2958 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.04 % Allowed : 22.64 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.74 (0.17), residues: 2640 helix: 3.61 (0.12), residues: 1776 sheet: 2.24 (0.49), residues: 156 loop : -0.67 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 85 TYR 0.016 0.001 TYR D 123 PHE 0.013 0.001 PHE D 302 TRP 0.009 0.001 TRP H 111 HIS 0.001 0.000 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00325 (21648) covalent geometry : angle 0.59052 (29296) hydrogen bonds : bond 0.04064 ( 1520) hydrogen bonds : angle 3.07214 ( 4416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8568 (mpp80) REVERT: H 301 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7475 (mmp80) REVERT: H 335 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 155 ARG cc_start: 0.8983 (mtm-85) cc_final: 0.8564 (mpp80) REVERT: B 301 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: B 335 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6697 (mp) REVERT: D 155 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8785 (mpp80) REVERT: E 301 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7467 (mmp80) REVERT: E 335 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6672 (mp) REVERT: F 155 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8570 (mpp80) REVERT: G 301 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7472 (mmp80) REVERT: G 335 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6695 (mp) outliers start: 45 outliers final: 12 residues processed: 210 average time/residue: 0.7810 time to fit residues: 183.0271 Evaluate side-chains 200 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 95 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 219 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 203 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.128844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074719 restraints weight = 34934.539| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.97 r_work: 0.2830 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21648 Z= 0.114 Angle : 0.596 9.818 29296 Z= 0.276 Chirality : 0.035 0.123 3184 Planarity : 0.003 0.044 3840 Dihedral : 3.592 38.048 2958 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.68 % Allowed : 23.28 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.82 (0.17), residues: 2640 helix: 3.68 (0.12), residues: 1776 sheet: 2.33 (0.50), residues: 156 loop : -0.70 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 63 TYR 0.013 0.001 TYR D 123 PHE 0.028 0.001 PHE D 324 TRP 0.009 0.001 TRP E 111 HIS 0.000 0.000 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00245 (21648) covalent geometry : angle 0.59578 (29296) hydrogen bonds : bond 0.03612 ( 1520) hydrogen bonds : angle 3.00441 ( 4416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8573 (mpp80) REVERT: H 301 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7468 (mmp80) REVERT: H 335 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6702 (mp) REVERT: A 155 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8575 (mpp80) REVERT: B 301 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7451 (mmp80) REVERT: B 335 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6680 (mp) REVERT: D 155 ARG cc_start: 0.9080 (mtm-85) cc_final: 0.8816 (mpp80) REVERT: E 301 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7466 (mmp80) REVERT: E 335 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6745 (mp) REVERT: F 155 ARG cc_start: 0.9004 (mtm-85) cc_final: 0.8578 (mpp80) REVERT: G 301 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: G 335 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6719 (mp) outliers start: 37 outliers final: 14 residues processed: 207 average time/residue: 0.7613 time to fit residues: 176.1388 Evaluate side-chains 203 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 262 optimal weight: 6.9990 chunk 259 optimal weight: 0.0040 chunk 206 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 252 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 156 optimal weight: 0.2980 chunk 214 optimal weight: 0.5980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.128804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074552 restraints weight = 34958.574| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.96 r_work: 0.2824 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21648 Z= 0.118 Angle : 0.619 11.182 29296 Z= 0.286 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.049 3840 Dihedral : 3.578 37.476 2958 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.86 % Allowed : 23.55 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.86 (0.17), residues: 2640 helix: 3.71 (0.12), residues: 1776 sheet: 2.33 (0.50), residues: 156 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 63 TYR 0.013 0.001 TYR D 123 PHE 0.012 0.001 PHE D 181 TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00260 (21648) covalent geometry : angle 0.61850 (29296) hydrogen bonds : bond 0.03624 ( 1520) hydrogen bonds : angle 2.98550 ( 4416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8999 (mtm-85) cc_final: 0.8572 (mpp80) REVERT: H 301 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7467 (mmp80) REVERT: A 155 ARG cc_start: 0.9008 (mtm-85) cc_final: 0.8580 (mpp80) REVERT: D 155 ARG cc_start: 0.9065 (mtm-85) cc_final: 0.8740 (mpp80) REVERT: E 301 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7463 (mmp80) REVERT: E 335 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6746 (mp) REVERT: F 155 ARG cc_start: 0.9003 (mtm-85) cc_final: 0.8576 (mpp80) REVERT: G 301 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7462 (mmp80) REVERT: G 335 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6745 (mp) outliers start: 41 outliers final: 24 residues processed: 198 average time/residue: 0.7886 time to fit residues: 174.2083 Evaluate side-chains 207 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 40 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.128283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073851 restraints weight = 34877.232| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.94 r_work: 0.2813 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21648 Z= 0.128 Angle : 0.630 10.846 29296 Z= 0.291 Chirality : 0.035 0.127 3184 Planarity : 0.003 0.044 3840 Dihedral : 3.597 37.237 2958 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 24.00 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.88 (0.17), residues: 2640 helix: 3.73 (0.12), residues: 1776 sheet: 2.31 (0.50), residues: 156 loop : -0.67 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 63 TYR 0.015 0.001 TYR D 123 PHE 0.030 0.001 PHE D 324 TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00290 (21648) covalent geometry : angle 0.63043 (29296) hydrogen bonds : bond 0.03760 ( 1520) hydrogen bonds : angle 2.99330 ( 4416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8519 (mpp80) REVERT: H 155 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8487 (mpp80) REVERT: H 301 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (mmp80) REVERT: A 155 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8518 (mpp80) REVERT: B 155 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8490 (mpp80) REVERT: D 155 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8705 (mpp80) REVERT: E 301 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: F 155 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8524 (mpp80) REVERT: G 155 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8483 (mpp80) REVERT: G 301 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7482 (mmp80) outliers start: 32 outliers final: 16 residues processed: 193 average time/residue: 0.7870 time to fit residues: 169.3246 Evaluate side-chains 195 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 328 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 128 optimal weight: 1.9990 chunk 213 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 211 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.128774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074489 restraints weight = 34897.594| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.92 r_work: 0.2821 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21648 Z= 0.120 Angle : 0.627 10.646 29296 Z= 0.290 Chirality : 0.035 0.158 3184 Planarity : 0.003 0.056 3840 Dihedral : 3.566 36.582 2958 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.31 % Allowed : 24.18 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.89 (0.17), residues: 2640 helix: 3.74 (0.12), residues: 1776 sheet: 2.34 (0.50), residues: 156 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 85 TYR 0.014 0.001 TYR D 123 PHE 0.012 0.001 PHE D 181 TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00266 (21648) covalent geometry : angle 0.62664 (29296) hydrogen bonds : bond 0.03609 ( 1520) hydrogen bonds : angle 2.97205 ( 4416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9471.68 seconds wall clock time: 161 minutes 55.36 seconds (9715.36 seconds total)