Starting phenix.real_space_refine on Wed May 21 08:54:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3p_17389/05_2025/8p3p_17389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3p_17389/05_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_17389/05_2025/8p3p_17389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3p_17389/05_2025/8p3p_17389.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3p_17389/05_2025/8p3p_17389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3p_17389/05_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-5687/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: 14.96, per 1000 atoms: 0.70 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: 4.88 Conformation dependent library (CDL) restraints added in 2.6 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: 2.07 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: 6.86 Time building geometry restraints manager: 5.75 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.610 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: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.040 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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: 72.430 ------------------------------------------------------------------------------- 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 : 2.345 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: 1.6301 time to fit residues: 370.9741 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 : 2.591 ------------------------------------------------------------------------------- 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 = 0.126956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073611 restraints weight = 34820.543| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.87 r_work: 0.2779 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 2.462 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: 0.7707 (t0) cc_final: 0.7482 (t0) REVERT: C 155 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8641 (mtm-85) REVERT: H 301 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7453 (mmp80) REVERT: A 152 ASP cc_start: 0.7701 (t0) cc_final: 0.7476 (t0) REVERT: A 155 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8637 (mtm-85) REVERT: B 301 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7458 (mmp80) REVERT: D 155 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8572 (mpp80) REVERT: E 301 ARG cc_start: 0.7908 (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: 0.8890 (mtm-85) cc_final: 0.8637 (mtm-85) REVERT: G 301 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7454 (mmp80) outliers start: 33 outliers final: 14 residues processed: 215 average time/residue: 1.6430 time to fit residues: 392.5968 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 : 2.404 ------------------------------------------------------------------------------- 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: 0.0050 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: 0.6980 chunk 255 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 209 optimal weight: 0.8980 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.127112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072394 restraints weight = 34900.228| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.92 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21648 Z= 0.152 Angle : 0.545 7.837 29296 Z= 0.267 Chirality : 0.036 0.121 3184 Planarity : 0.003 0.033 3840 Dihedral : 3.697 37.375 2958 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 21.15 % Favored : 76.40 % 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: 3.63 (0.17), residues: 2640 helix: 3.48 (0.12), residues: 1780 sheet: 2.31 (0.49), residues: 156 loop : -0.63 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.001 0.000 HIS C 189 PHE 0.013 0.001 PHE C 302 TYR 0.017 0.001 TYR C 123 ARG 0.007 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1520) hydrogen bonds : angle 3.17044 ( 4416) covalent geometry : bond 0.00349 (21648) covalent geometry : angle 0.54545 (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 254 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 2.580 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: 0.8945 (mtm-85) cc_final: 0.8660 (mtm-85) REVERT: H 301 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7495 (mmp80) REVERT: H 335 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 155 ARG cc_start: 0.8943 (mtm-85) cc_final: 0.8657 (mtm-85) REVERT: B 301 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7500 (mmp80) REVERT: B 335 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6667 (mp) REVERT: D 155 ARG cc_start: 0.8956 (mtm-85) cc_final: 0.8530 (mpp80) REVERT: E 301 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7472 (mmp80) REVERT: E 335 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6666 (mp) REVERT: F 155 ARG cc_start: 0.8945 (mtm-85) cc_final: 0.8661 (mtm-85) REVERT: G 301 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7466 (mmp80) REVERT: G 335 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6662 (mp) outliers start: 54 outliers final: 16 residues processed: 226 average time/residue: 1.5228 time to fit residues: 384.7059 Evaluate side-chains 208 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 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 E residue 36 MET Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 147 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 263 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 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 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 = 0.3868 r_free = 0.3868 target = 0.127460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074112 restraints weight = 35022.467| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.92 r_work: 0.2793 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21648 Z= 0.130 Angle : 0.540 8.022 29296 Z= 0.262 Chirality : 0.035 0.159 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.640 37.250 2958 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.90 % Allowed : 21.06 % Favored : 76.04 % 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: 3.69 (0.17), residues: 2640 helix: 3.54 (0.12), residues: 1776 sheet: 2.39 (0.50), residues: 156 loop : -0.66 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 111 HIS 0.001 0.000 HIS C 189 PHE 0.026 0.001 PHE C 324 TYR 0.016 0.001 TYR F 123 ARG 0.009 0.000 ARG G 85 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1520) hydrogen bonds : angle 3.10208 ( 4416) covalent geometry : bond 0.00289 (21648) covalent geometry : angle 0.54047 (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 257 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 2.501 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: 0.8957 (mtm-85) cc_final: 0.8510 (mpp80) REVERT: H 301 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7440 (mmp80) REVERT: H 335 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6693 (mp) REVERT: A 155 ARG cc_start: 0.8956 (mtm-85) cc_final: 0.8507 (mpp80) REVERT: B 301 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7444 (mmp80) REVERT: B 335 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6693 (mp) REVERT: D 155 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8615 (mtm-85) REVERT: E 301 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7452 (mmp80) REVERT: E 335 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6693 (mp) REVERT: F 155 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8508 (mpp80) REVERT: G 301 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7454 (mmp80) outliers start: 64 outliers final: 21 residues processed: 227 average time/residue: 1.3266 time to fit residues: 340.7494 Evaluate side-chains 212 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain 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 307 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain 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 301 ARG Chi-restraints excluded: chain G residue 307 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 0.3980 chunk 262 optimal weight: 0.8980 chunk 254 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.126938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071916 restraints weight = 35108.185| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.98 r_work: 0.2766 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21648 Z= 0.163 Angle : 0.571 9.294 29296 Z= 0.274 Chirality : 0.036 0.121 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.713 38.021 2958 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.99 % Allowed : 21.47 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.64 (0.17), residues: 2640 helix: 3.51 (0.12), residues: 1780 sheet: 2.16 (0.48), residues: 160 loop : -0.67 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.001 0.001 HIS C 189 PHE 0.014 0.001 PHE A 302 TYR 0.018 0.002 TYR C 123 ARG 0.010 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1520) hydrogen bonds : angle 3.12097 ( 4416) covalent geometry : bond 0.00378 (21648) covalent geometry : angle 0.57070 (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 261 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 2.365 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: 0.8979 (mtm-85) cc_final: 0.8545 (mpp80) REVERT: H 301 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7477 (mmp80) REVERT: H 335 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6704 (mp) REVERT: A 155 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8531 (mpp80) REVERT: B 301 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7481 (mmp80) REVERT: B 335 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6678 (mp) REVERT: D 155 ARG cc_start: 0.9012 (mtm-85) cc_final: 0.8633 (mpp80) REVERT: E 301 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7483 (mmp80) REVERT: E 335 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6699 (mp) REVERT: F 155 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8532 (mpp80) REVERT: G 301 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7484 (mmp80) REVERT: G 335 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6670 (mp) outliers start: 66 outliers final: 20 residues processed: 226 average time/residue: 1.5109 time to fit residues: 381.8350 Evaluate side-chains 212 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 256 MET Chi-restraints excluded: chain H residue 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 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: 8.9990 chunk 131 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 189 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 155 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.128457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074185 restraints weight = 34890.892| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.95 r_work: 0.2819 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21648 Z= 0.113 Angle : 0.554 8.917 29296 Z= 0.263 Chirality : 0.035 0.121 3184 Planarity : 0.003 0.034 3840 Dihedral : 3.600 37.673 2958 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 22.46 % 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: 3.77 (0.17), residues: 2640 helix: 3.63 (0.12), residues: 1776 sheet: 2.36 (0.50), residues: 156 loop : -0.68 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.000 0.000 HIS G 189 PHE 0.027 0.001 PHE F 324 TYR 0.014 0.001 TYR D 123 ARG 0.010 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 1520) hydrogen bonds : angle 3.03790 ( 4416) covalent geometry : bond 0.00243 (21648) covalent geometry : angle 0.55442 (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 246 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 2.644 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: 0.8998 (mtm-85) cc_final: 0.8650 (mpp80) REVERT: H 106 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8606 (ttm) REVERT: H 301 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7467 (mmp80) REVERT: A 155 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8560 (mpp80) REVERT: B 63 ARG cc_start: 0.8351 (mtm110) cc_final: 0.8147 (mtp-110) REVERT: B 106 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (ttm) REVERT: B 155 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8389 (mpp80) REVERT: B 301 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7470 (mmp80) REVERT: D 155 ARG cc_start: 0.9050 (mtm-85) cc_final: 0.8574 (mpp80) REVERT: E 106 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8601 (ttm) REVERT: E 301 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7454 (mmp80) REVERT: F 155 ARG cc_start: 0.9005 (mtm-85) cc_final: 0.8569 (mpp80) REVERT: G 106 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8604 (ttm) REVERT: G 155 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8383 (mpp80) REVERT: G 301 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7478 (mmp80) REVERT: G 335 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6699 (mp) outliers start: 47 outliers final: 17 residues processed: 218 average time/residue: 1.4618 time to fit residues: 357.1736 Evaluate side-chains 214 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 106 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 307 TYR Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 307 TYR 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 106 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 307 TYR Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 106 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 186 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 241 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 259 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.126357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.071400 restraints weight = 34888.812| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.95 r_work: 0.2762 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21648 Z= 0.192 Angle : 0.598 9.300 29296 Z= 0.286 Chirality : 0.037 0.121 3184 Planarity : 0.003 0.036 3840 Dihedral : 3.769 39.378 2958 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.22 % Allowed : 23.01 % Favored : 74.77 % 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: 3.71 (0.17), residues: 2640 helix: 3.58 (0.12), residues: 1776 sheet: 2.14 (0.48), residues: 160 loop : -0.67 (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 A 189 PHE 0.015 0.001 PHE A 302 TYR 0.019 0.002 TYR D 123 ARG 0.009 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 1520) hydrogen bonds : angle 3.11853 ( 4416) covalent geometry : bond 0.00453 (21648) covalent geometry : angle 0.59764 (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 242 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8543 (mpp80) REVERT: H 301 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7466 (mmp80) REVERT: H 335 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6687 (mp) REVERT: A 155 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8546 (mpp80) REVERT: B 155 ARG cc_start: 0.9022 (mtm-85) cc_final: 0.8388 (mpp80) REVERT: B 301 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: B 335 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6689 (mp) REVERT: D 155 ARG cc_start: 0.9042 (mtm-85) cc_final: 0.8783 (mpp80) REVERT: E 301 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7470 (mmp80) REVERT: E 335 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6688 (mp) REVERT: F 155 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8546 (mpp80) REVERT: G 155 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8385 (mpp80) REVERT: G 301 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7466 (mmp80) REVERT: G 335 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6685 (mp) outliers start: 49 outliers final: 11 residues processed: 217 average time/residue: 1.4410 time to fit residues: 354.3208 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 : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 301 ARG Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 301 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 237 HIS Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 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: 3.9990 chunk 224 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN G 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072510 restraints weight = 35163.396| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.98 r_work: 0.2785 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1181 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= 0.141 Angle : 0.610 10.002 29296 Z= 0.285 Chirality : 0.036 0.124 3184 Planarity : 0.003 0.032 3840 Dihedral : 3.716 39.552 2958 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.04 % Allowed : 23.10 % 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: 3.75 (0.17), residues: 2640 helix: 3.61 (0.12), residues: 1780 sheet: 2.20 (0.48), residues: 160 loop : -0.69 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 111 HIS 0.001 0.000 HIS A 189 PHE 0.029 0.001 PHE D 324 TYR 0.016 0.001 TYR F 123 ARG 0.007 0.000 ARG B 63 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1520) hydrogen bonds : angle 3.07510 ( 4416) covalent geometry : bond 0.00323 (21648) covalent geometry : angle 0.60996 (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: 45 poor density : 185 time to evaluate : 2.508 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: 0.8999 (mtm-85) cc_final: 0.8547 (mpp80) REVERT: H 155 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8466 (mpp80) REVERT: H 301 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7466 (mmp80) REVERT: A 155 ARG cc_start: 0.8979 (mtm-85) cc_final: 0.8545 (mpp80) REVERT: B 155 ARG cc_start: 0.9039 (mtm-85) cc_final: 0.8426 (mpp80) REVERT: B 301 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7465 (mmp80) REVERT: D 155 ARG cc_start: 0.9073 (mtm-85) cc_final: 0.8729 (mpp80) REVERT: E 155 ARG cc_start: 0.9026 (mtm-85) cc_final: 0.8466 (mpp80) REVERT: E 301 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7471 (mmp80) REVERT: F 155 ARG cc_start: 0.9001 (mtm-85) cc_final: 0.8551 (mpp80) REVERT: G 155 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8420 (mpp80) REVERT: G 301 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7469 (mmp80) REVERT: G 335 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6685 (mp) outliers start: 45 outliers final: 17 residues processed: 206 average time/residue: 1.4101 time to fit residues: 326.9078 Evaluate side-chains 202 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 291 THR 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 A residue 237 HIS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 291 THR 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 F residue 237 HIS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 79 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 225 optimal weight: 0.1980 chunk 34 optimal weight: 9.9990 chunk 241 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073824 restraints weight = 35018.953| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.95 r_work: 0.2806 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.040 21648 Z= 0.125 Angle : 0.613 10.487 29296 Z= 0.287 Chirality : 0.035 0.124 3184 Planarity : 0.003 0.040 3840 Dihedral : 3.667 38.982 2958 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.77 % Allowed : 23.46 % Favored : 74.77 % 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: 3.82 (0.17), residues: 2640 helix: 3.68 (0.12), residues: 1776 sheet: 2.30 (0.50), residues: 156 loop : -0.68 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.001 0.000 HIS D 189 PHE 0.013 0.001 PHE H 181 TYR 0.014 0.001 TYR D 123 ARG 0.014 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1520) hydrogen bonds : angle 3.03625 ( 4416) covalent geometry : bond 0.00279 (21648) covalent geometry : angle 0.61292 (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 228 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 2.432 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: 0.8995 (mtm-85) cc_final: 0.8522 (mpp80) REVERT: H 155 ARG cc_start: 0.9049 (mtm-85) cc_final: 0.8491 (mpp80) REVERT: H 301 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7490 (mmp80) REVERT: A 155 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8524 (mpp80) REVERT: B 155 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8404 (mpp80) REVERT: B 301 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7485 (mmp80) REVERT: D 155 ARG cc_start: 0.9065 (mtm-85) cc_final: 0.8725 (mpp80) REVERT: E 63 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8089 (mtp-110) REVERT: E 155 ARG cc_start: 0.9051 (mtm-85) cc_final: 0.8491 (mpp80) REVERT: E 301 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7492 (mmp80) REVERT: F 155 ARG cc_start: 0.8999 (mtm-85) cc_final: 0.8532 (mpp80) REVERT: G 155 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8403 (mpp80) REVERT: G 301 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7488 (mmp80) outliers start: 39 outliers final: 15 residues processed: 203 average time/residue: 1.5013 time to fit residues: 342.8838 Evaluate side-chains 205 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 291 THR 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 237 HIS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 291 THR 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 F residue 237 HIS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET 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 120 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 189 optimal weight: 4.9990 chunk 147 optimal weight: 0.0770 chunk 193 optimal weight: 0.0000 chunk 101 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 overall best weight: 0.6544 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.127404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074337 restraints weight = 34917.830| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.88 r_work: 0.2795 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1299 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 : 0.631 11.898 29296 Z= 0.294 Chirality : 0.035 0.137 3184 Planarity : 0.003 0.056 3840 Dihedral : 3.672 38.901 2958 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.31 % Allowed : 24.23 % Favored : 74.46 % 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: 3.66 (0.12), residues: 1780 sheet: 2.26 (0.49), residues: 156 loop : -0.69 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 111 HIS 0.001 0.000 HIS D 189 PHE 0.029 0.001 PHE A 324 TYR 0.016 0.001 TYR D 123 ARG 0.013 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1520) hydrogen bonds : angle 3.04009 ( 4416) covalent geometry : bond 0.00305 (21648) covalent geometry : angle 0.63089 (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 214 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 2.615 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: 0.8975 (mtm-85) cc_final: 0.8512 (mpp80) REVERT: H 155 ARG cc_start: 0.9049 (mtm-85) cc_final: 0.8490 (mpp80) REVERT: H 301 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7474 (mmp80) REVERT: A 155 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8513 (mpp80) REVERT: B 155 ARG cc_start: 0.9055 (mtm-85) cc_final: 0.8419 (mpp80) REVERT: B 301 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7476 (mmp80) REVERT: D 155 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8702 (mpp80) REVERT: E 155 ARG cc_start: 0.9050 (mtm-85) cc_final: 0.8486 (mpp80) REVERT: E 301 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7478 (mmp80) REVERT: F 155 ARG cc_start: 0.8977 (mtm-85) cc_final: 0.8517 (mpp80) REVERT: G 155 ARG cc_start: 0.9053 (mtm-85) cc_final: 0.8416 (mpp80) REVERT: G 301 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7476 (mmp80) outliers start: 29 outliers final: 16 residues processed: 198 average time/residue: 1.5907 time to fit residues: 360.0366 Evaluate side-chains 203 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 HIS Chi-restraints excluded: chain C residue 291 THR 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 A residue 237 HIS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain D residue 237 HIS Chi-restraints excluded: chain D residue 291 THR 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 F residue 237 HIS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 256 MET 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: 0.6980 chunk 188 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 7 optimal weight: 0.0040 chunk 161 optimal weight: 0.8980 overall best weight: 0.4250 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.128769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074544 restraints weight = 34958.739| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.98 r_work: 0.2823 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21648 Z= 0.119 Angle : 0.623 10.864 29296 Z= 0.290 Chirality : 0.035 0.126 3184 Planarity : 0.003 0.048 3840 Dihedral : 3.592 37.794 2958 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.13 % Allowed : 24.46 % Favored : 74.41 % 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: 3.87 (0.17), residues: 2640 helix: 3.73 (0.12), residues: 1776 sheet: 2.30 (0.50), residues: 156 loop : -0.70 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.001 0.000 HIS A 189 PHE 0.013 0.001 PHE C 181 TYR 0.013 0.001 TYR D 123 ARG 0.012 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1520) hydrogen bonds : angle 2.98910 ( 4416) covalent geometry : bond 0.00262 (21648) covalent geometry : angle 0.62348 (29296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16967.22 seconds wall clock time: 293 minutes 3.95 seconds (17583.95 seconds total)