Starting phenix.real_space_refine on Wed Jun 18 12:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3p_17389/06_2025/8p3p_17389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3p_17389/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3p_17389/06_2025/8p3p_17389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3p_17389/06_2025/8p3p_17389.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3p_17389/06_2025/8p3p_17389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3p_17389/06_2025/8p3p_17389.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.26, per 1000 atoms: 0.72 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: 5.10 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.86 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: 6.64 Time building geometry restraints manager: 6.09 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: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.640 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: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 49.450 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.880 ------------------------------------------------------------------------------- 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 : 5.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 111 HIS 0.001 0.000 HIS F 237 PHE 0.027 0.001 PHE A 324 TYR 0.014 0.001 TYR C 123 ARG 0.009 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.11442 ( 1520) hydrogen bonds : angle 4.33442 ( 4416) covalent geometry : bond 0.00288 (21648) covalent geometry : angle 0.62593 (29296) *********************** 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 : 2.417 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: 1.7082 time to fit residues: 387.1115 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 : 2.323 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 206 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.126949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073638 restraints weight = 34823.091| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.85 r_work: 0.2780 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21648 Z= 0.163 Angle : 0.556 7.614 29296 Z= 0.275 Chirality : 0.036 0.151 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.905 36.775 2968 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.49 % Allowed : 21.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.17), residues: 2640 helix: 3.46 (0.12), residues: 1780 sheet: 2.33 (0.49), residues: 156 loop : -0.70 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 111 HIS 0.002 0.001 HIS B 237 PHE 0.020 0.001 PHE A 324 TYR 0.017 0.002 TYR C 123 ARG 0.005 0.000 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 1520) hydrogen bonds : angle 3.27237 ( 4416) covalent geometry : bond 0.00369 (21648) covalent geometry : angle 0.55619 (29296) *********************** 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 233 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 2.460 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: 0.7708 (t0) cc_final: 0.7483 (t0) REVERT: C 155 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8643 (mtm-85) REVERT: H 301 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7452 (mmp80) REVERT: A 152 ASP cc_start: 0.7701 (t0) cc_final: 0.7476 (t0) REVERT: A 155 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8640 (mtm-85) REVERT: B 301 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7457 (mmp80) REVERT: D 155 ARG cc_start: 0.8934 (mtm-85) cc_final: 0.8574 (mpp80) REVERT: E 301 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7456 (mmp80) REVERT: F 152 ASP cc_start: 0.7707 (t0) cc_final: 0.7485 (t0) REVERT: F 155 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8639 (mtm-85) REVERT: G 301 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7453 (mmp80) outliers start: 33 outliers final: 14 residues processed: 215 average time/residue: 1.7925 time to fit residues: 426.2265 Evaluate side-chains 206 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET 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 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 D residue 68 MET Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain F residue 68 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 254 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 209 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.070218 restraints weight = 34992.638| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.03 r_work: 0.2738 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21648 Z= 0.225 Angle : 0.579 8.111 29296 Z= 0.286 Chirality : 0.038 0.122 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.868 39.135 2958 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.26 % Allowed : 21.01 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.17), residues: 2640 helix: 3.40 (0.12), residues: 1776 sheet: 2.06 (0.48), residues: 160 loop : -0.60 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.002 0.001 HIS C 189 PHE 0.015 0.001 PHE A 302 TYR 0.019 0.002 TYR A 123 ARG 0.008 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 1520) hydrogen bonds : angle 3.25717 ( 4416) covalent geometry : bond 0.00532 (21648) covalent geometry : angle 0.57909 (29296) *********************** 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 246 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 2.332 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: 0.8914 (mtm-85) cc_final: 0.8606 (mtm-85) REVERT: H 301 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7535 (mmp80) REVERT: H 335 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6669 (mp) REVERT: A 155 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8602 (mtm-85) REVERT: B 301 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7546 (mmp80) REVERT: B 335 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6670 (mp) REVERT: D 155 ARG cc_start: 0.8964 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: E 301 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7548 (mmp80) REVERT: E 335 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6670 (mp) REVERT: F 155 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8613 (mtm-85) REVERT: G 301 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7548 (mmp80) REVERT: G 335 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6668 (mp) outliers start: 50 outliers final: 18 residues processed: 218 average time/residue: 1.7120 time to fit residues: 415.1280 Evaluate side-chains 210 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET 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 68 MET 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 D residue 68 MET 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 68 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 30.0000 chunk 263 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.127161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072438 restraints weight = 35177.475| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.94 r_work: 0.2777 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0944 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= 0.140 Angle : 0.550 8.098 29296 Z= 0.268 Chirality : 0.036 0.121 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.757 39.048 2958 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.54 % Allowed : 21.78 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.17), residues: 2640 helix: 3.47 (0.12), residues: 1780 sheet: 2.24 (0.49), residues: 160 loop : -0.72 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.001 0.000 HIS F 237 PHE 0.026 0.001 PHE A 324 TYR 0.016 0.001 TYR A 123 ARG 0.009 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 1520) hydrogen bonds : angle 3.16050 ( 4416) covalent geometry : bond 0.00314 (21648) covalent geometry : angle 0.55003 (29296) *********************** 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 253 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 3.593 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: 0.8944 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: H 301 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7458 (mmp80) REVERT: H 335 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 155 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8593 (mtm-85) REVERT: B 256 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (mmp) REVERT: B 301 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7448 (mmp80) REVERT: B 335 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6675 (mp) REVERT: D 155 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8632 (mpp80) REVERT: E 301 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7451 (mmp80) REVERT: E 335 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6674 (mp) REVERT: F 155 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: G 301 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7445 (mmp80) REVERT: G 335 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6690 (mp) outliers start: 56 outliers final: 18 residues processed: 226 average time/residue: 1.9175 time to fit residues: 487.4459 Evaluate side-chains 214 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS 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 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 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 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 256 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 F residue 325 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.126057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070832 restraints weight = 35131.819| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.97 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: 0.8266 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21648 Z= 0.196 Angle : 0.583 8.347 29296 Z= 0.284 Chirality : 0.037 0.124 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.849 40.401 2958 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.90 % Allowed : 21.69 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.17), residues: 2640 helix: 3.42 (0.12), residues: 1776 sheet: 2.08 (0.48), residues: 160 loop : -0.74 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.002 0.001 HIS C 189 PHE 0.015 0.001 PHE A 302 TYR 0.019 0.002 TYR D 123 ARG 0.008 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 1520) hydrogen bonds : angle 3.19686 ( 4416) covalent geometry : bond 0.00461 (21648) covalent geometry : angle 0.58308 (29296) *********************** 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 253 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 2.230 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: 0.8958 (mtm-85) cc_final: 0.8516 (mpp80) REVERT: H 301 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7522 (mmp80) REVERT: H 335 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6686 (mp) REVERT: A 155 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8523 (mpp80) REVERT: B 301 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7525 (mmp80) REVERT: B 335 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6685 (mp) REVERT: D 155 ARG cc_start: 0.8997 (mtm-85) cc_final: 0.8613 (mpp80) REVERT: E 301 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7524 (mmp80) REVERT: E 335 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6688 (mp) REVERT: F 155 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8524 (mpp80) REVERT: G 301 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7523 (mmp80) REVERT: G 335 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6686 (mp) outliers start: 64 outliers final: 17 residues processed: 221 average time/residue: 1.5753 time to fit residues: 389.0296 Evaluate side-chains 201 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS 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 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 A residue 325 LEU 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 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 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 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 128 optimal weight: 0.5980 chunk 189 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073761 restraints weight = 34773.713| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.85 r_work: 0.2787 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21648 Z= 0.134 Angle : 0.573 8.866 29296 Z= 0.275 Chirality : 0.035 0.126 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.741 39.931 2958 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.26 % Allowed : 22.06 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.17), residues: 2640 helix: 3.53 (0.12), residues: 1780 sheet: 2.21 (0.49), residues: 160 loop : -0.72 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.003 0.000 HIS E 237 PHE 0.027 0.001 PHE C 324 TYR 0.016 0.001 TYR F 123 ARG 0.011 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 1520) hydrogen bonds : angle 3.11031 ( 4416) covalent geometry : bond 0.00300 (21648) covalent geometry : angle 0.57335 (29296) *********************** 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 245 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 2.220 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: C 155 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8508 (mpp80) REVERT: H 301 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7457 (mmp80) REVERT: H 335 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6691 (mp) REVERT: A 155 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8504 (mpp80) REVERT: B 301 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7458 (mmp80) REVERT: B 335 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6685 (mp) REVERT: D 155 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8546 (mpp80) REVERT: E 301 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7455 (mmp80) REVERT: F 155 ARG cc_start: 0.8987 (mtm-85) cc_final: 0.8511 (mpp80) REVERT: G 301 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7455 (mmp80) outliers start: 50 outliers final: 12 residues processed: 227 average time/residue: 1.5202 time to fit residues: 386.0477 Evaluate side-chains 202 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS 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 301 ARG Chi-restraints excluded: chain H residue 335 LEU 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 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 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 301 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 186 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 245 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 259 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.127156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074186 restraints weight = 34754.999| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.87 r_work: 0.2794 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21648 Z= 0.133 Angle : 0.591 9.876 29296 Z= 0.279 Chirality : 0.035 0.124 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.712 40.214 2958 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.72 % Allowed : 23.41 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.17), residues: 2640 helix: 3.59 (0.12), residues: 1776 sheet: 2.29 (0.49), residues: 156 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.003 0.000 HIS E 237 PHE 0.013 0.001 PHE D 181 TYR 0.015 0.001 TYR A 123 ARG 0.009 0.000 ARG G 85 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1520) hydrogen bonds : angle 3.08141 ( 4416) covalent geometry : bond 0.00299 (21648) covalent geometry : angle 0.59150 (29296) *********************** 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 226 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 2.378 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: 0.8987 (mtm-85) cc_final: 0.8569 (mpp80) REVERT: H 301 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7477 (mmp80) REVERT: A 155 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8566 (mpp80) REVERT: B 155 ARG cc_start: 0.9005 (mtm-85) cc_final: 0.8328 (mpp80) REVERT: B 301 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7484 (mmp80) REVERT: D 152 ASP cc_start: 0.7759 (t0) cc_final: 0.7518 (t0) REVERT: D 155 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8517 (mpp80) REVERT: E 301 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7451 (mmp80) REVERT: F 155 ARG cc_start: 0.8988 (mtm-85) cc_final: 0.8571 (mpp80) REVERT: G 155 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8320 (mpp80) REVERT: G 301 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7451 (mmp80) REVERT: G 335 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6685 (mp) outliers start: 38 outliers final: 15 residues processed: 205 average time/residue: 1.5813 time to fit residues: 367.8097 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 : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS 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 263 MET Chi-restraints excluded: chain H residue 301 ARG 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 263 MET Chi-restraints excluded: chain B residue 301 ARG 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 F residue 210 LYS 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 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 63 optimal weight: 2.9990 chunk 224 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 221 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073245 restraints weight = 35083.656| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.93 r_work: 0.2793 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21648 Z= 0.134 Angle : 0.609 10.955 29296 Z= 0.285 Chirality : 0.035 0.123 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.689 40.282 2958 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.13 % Allowed : 23.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.17), residues: 2640 helix: 3.62 (0.12), residues: 1776 sheet: 2.30 (0.50), residues: 156 loop : -0.72 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 111 HIS 0.002 0.000 HIS E 237 PHE 0.029 0.001 PHE D 324 TYR 0.015 0.001 TYR C 123 ARG 0.006 0.000 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 1520) hydrogen bonds : angle 3.06323 ( 4416) covalent geometry : bond 0.00303 (21648) covalent geometry : angle 0.60899 (29296) *********************** 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 230 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 2.250 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: 0.8985 (mtm-85) cc_final: 0.8509 (mpp80) REVERT: H 155 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8388 (mpp80) REVERT: H 301 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7470 (mmp80) REVERT: H 335 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6719 (mp) REVERT: A 155 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8521 (mpp80) REVERT: B 155 ARG cc_start: 0.8996 (mtm-85) cc_final: 0.8292 (mpp80) REVERT: B 301 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7475 (mmp80) REVERT: B 335 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6713 (mp) REVERT: D 155 ARG cc_start: 0.9049 (mtm-85) cc_final: 0.8686 (mpp80) REVERT: E 155 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8430 (mpp80) REVERT: E 301 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: F 155 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8525 (mpp80) REVERT: G 155 ARG cc_start: 0.8995 (mtm-85) cc_final: 0.8290 (mpp80) REVERT: G 301 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7469 (mmp80) outliers start: 47 outliers final: 20 residues processed: 208 average time/residue: 1.7493 time to fit residues: 408.9567 Evaluate side-chains 213 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 LYS 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 263 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 237 HIS Chi-restraints excluded: chain A residue 325 LEU 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 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 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain F residue 210 LYS 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 301 ARG Chi-restraints excluded: chain G residue 307 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 263 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 241 optimal weight: 0.3980 chunk 147 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.128490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074226 restraints weight = 34978.146| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.95 r_work: 0.2818 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1261 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= 0.121 Angle : 0.618 11.448 29296 Z= 0.289 Chirality : 0.035 0.122 3184 Planarity : 0.003 0.043 3840 Dihedral : 3.649 39.487 2958 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.17 % Allowed : 23.14 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.17), residues: 2640 helix: 3.65 (0.12), residues: 1776 sheet: 2.36 (0.50), residues: 156 loop : -0.74 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.002 0.000 HIS E 237 PHE 0.013 0.001 PHE C 181 TYR 0.014 0.001 TYR F 123 ARG 0.011 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1520) hydrogen bonds : angle 3.03465 ( 4416) covalent geometry : bond 0.00268 (21648) covalent geometry : angle 0.61807 (29296) *********************** 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 237 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 3.182 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: 0.8982 (mtm-85) cc_final: 0.8513 (mpp80) REVERT: H 155 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8404 (mpp80) REVERT: H 301 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7456 (mmp80) REVERT: H 335 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 155 ARG cc_start: 0.8983 (mtm-85) cc_final: 0.8515 (mpp80) REVERT: B 155 ARG cc_start: 0.9012 (mtm-85) cc_final: 0.8348 (mpp80) REVERT: B 301 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7457 (mmp80) REVERT: B 335 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6714 (mp) REVERT: D 155 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8724 (mpp80) REVERT: E 155 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8395 (mpp80) REVERT: E 301 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7467 (mmp80) REVERT: F 155 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8518 (mpp80) REVERT: G 155 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8339 (mpp80) REVERT: G 301 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7464 (mmp80) outliers start: 48 outliers final: 15 residues processed: 217 average time/residue: 1.4223 time to fit residues: 347.5162 Evaluate side-chains 205 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 2.293 ------------------------------------------------------------------------------- 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 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 233 ILE 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 F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.126805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.071676 restraints weight = 35018.064| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.97 r_work: 0.2761 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21648 Z= 0.177 Angle : 0.662 12.315 29296 Z= 0.311 Chirality : 0.037 0.178 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.796 40.728 2958 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.18 % Allowed : 24.09 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.17), residues: 2640 helix: 3.61 (0.12), residues: 1772 sheet: 2.16 (0.48), residues: 160 loop : -0.77 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.003 0.001 HIS E 237 PHE 0.028 0.002 PHE F 324 TYR 0.018 0.002 TYR D 123 ARG 0.014 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1520) hydrogen bonds : angle 3.11549 ( 4416) covalent geometry : bond 0.00417 (21648) covalent geometry : angle 0.66222 (29296) ********************** 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 206 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 3.008 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: C 155 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8462 (mpp80) REVERT: H 155 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8489 (mpp80) REVERT: H 301 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7459 (mmp80) REVERT: H 335 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6756 (mp) REVERT: A 155 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8460 (mpp80) REVERT: B 301 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: B 335 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6756 (mp) REVERT: D 155 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8683 (mpp80) REVERT: E 155 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8489 (mpp80) REVERT: E 301 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7461 (mmp80) REVERT: F 155 ARG cc_start: 0.8970 (mtm-85) cc_final: 0.8464 (mpp80) REVERT: G 301 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7459 (mmp80) outliers start: 26 outliers final: 13 residues processed: 192 average time/residue: 1.8576 time to fit residues: 411.0659 Evaluate side-chains 199 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 233 ILE 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 233 ILE Chi-restraints excluded: chain E residue 263 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 233 ILE Chi-restraints excluded: chain G residue 301 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 52 optimal weight: 0.5980 chunk 188 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 187 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 7 optimal weight: 0.0270 chunk 161 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073418 restraints weight = 34907.369| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.97 r_work: 0.2807 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1340 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= 0.123 Angle : 0.637 11.000 29296 Z= 0.295 Chirality : 0.035 0.128 3184 Planarity : 0.003 0.051 3840 Dihedral : 3.674 39.737 2958 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.36 % Allowed : 23.69 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.17), residues: 2640 helix: 3.67 (0.12), residues: 1776 sheet: 2.33 (0.50), residues: 156 loop : -0.71 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.001 0.000 HIS E 237 PHE 0.013 0.001 PHE E 181 TYR 0.014 0.001 TYR F 123 ARG 0.013 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1520) hydrogen bonds : angle 3.04081 ( 4416) covalent geometry : bond 0.00272 (21648) covalent geometry : angle 0.63674 (29296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18633.40 seconds wall clock time: 321 minutes 26.13 seconds (19286.13 seconds total)