Starting phenix.real_space_refine on Thu Jul 31 19:21:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyb_29563/07_2025/8fyb_29563.cif" } resolution = 3.1 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= -0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 571 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 135 5.49 5 S 32 5.16 5 C 8099 2.51 5 N 2441 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13486 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 737 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2414 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "F" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2188 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "G" Number of atoms: 1089 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 52, 1067 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} Conformer: "B" Number of residues, atoms: 52, 1067 Classifications: {'DNA': 52} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 51} bond proxies already assigned to first conformer: 1170 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "J" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 742 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "I" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 348 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DG G 29 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B DG G 29 " occ=0.50 Time building chain proxies: 9.30, per 1000 atoms: 0.69 Number of scatterers: 13486 At special positions: 0 Unit cell: (123.765, 97.005, 163.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 135 15.00 O 2779 8.00 N 2441 7.00 C 8099 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: 3.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 51.5% alpha, 14.4% beta 33 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.838A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 Processing helix chain 'B' and resid 139 through 162 Processing helix chain 'B' and resid 180 through 205 removed outlier: 3.591A pdb=" N LEU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 231 removed outlier: 4.028A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.535A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 4.084A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.643A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.830A pdb=" N LYS C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 204 removed outlier: 3.799A pdb=" N ALA C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.687A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.688A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.790A pdb=" N MET E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 4.379A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 139 through 162 Processing helix chain 'E' and resid 180 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 4.771A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 250 through 266 removed outlier: 4.022A pdb=" N LEU E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.854A pdb=" N LYS E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.703A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.635A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 removed outlier: 3.681A pdb=" N ALA F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 244 removed outlier: 3.767A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 235 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Proline residue: F 236 - end of helix Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.939A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.717A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA E 30 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N SER E 67 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.608A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 22 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.988A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA6, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 27 removed outlier: 6.395A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 80 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C 85 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 5.806A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.049A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR E 26 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 47 through 49 removed outlier: 4.078A pdb=" N ASN E 308 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 27 removed outlier: 6.463A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL F 82 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY F 85 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3437 1.33 - 1.45: 3290 1.45 - 1.57: 6968 1.57 - 1.69: 269 1.69 - 1.82: 62 Bond restraints: 14026 Sorted by residual: bond pdb=" CA TRP E 166 " pdb=" C TRP E 166 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.18e-02 7.18e+03 3.38e+00 bond pdb=" CA ARG E 169 " pdb=" C ARG E 169 " ideal model delta sigma weight residual 1.523 1.502 0.022 1.34e-02 5.57e+03 2.62e+00 bond pdb=" C3' DG G 8 " pdb=" O3' DG G 8 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CA VAL E 170 " pdb=" C VAL E 170 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.27e-02 6.20e+03 1.77e+00 bond pdb=" CA TYR E 171 " pdb=" C TYR E 171 " ideal model delta sigma weight residual 1.525 1.508 0.016 1.25e-02 6.40e+03 1.69e+00 ... (remaining 14021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19117 1.82 - 3.64: 414 3.64 - 5.47: 34 5.47 - 7.29: 6 7.29 - 9.11: 2 Bond angle restraints: 19573 Sorted by residual: angle pdb=" N LYS E 167 " pdb=" CA LYS E 167 " pdb=" C LYS E 167 " ideal model delta sigma weight residual 110.53 102.86 7.67 1.29e+00 6.01e-01 3.54e+01 angle pdb=" N LYS E 168 " pdb=" CA LYS E 168 " pdb=" C LYS E 168 " ideal model delta sigma weight residual 110.35 117.00 -6.65 1.36e+00 5.41e-01 2.39e+01 angle pdb=" N TRP E 166 " pdb=" CA TRP E 166 " pdb=" C TRP E 166 " ideal model delta sigma weight residual 107.37 116.48 -9.11 2.07e+00 2.33e-01 1.94e+01 angle pdb=" CA PRO E 165 " pdb=" C PRO E 165 " pdb=" N TRP E 166 " ideal model delta sigma weight residual 114.75 119.47 -4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA PRO E 165 " pdb=" C PRO E 165 " pdb=" O PRO E 165 " ideal model delta sigma weight residual 122.31 117.91 4.40 1.41e+00 5.03e-01 9.75e+00 ... (remaining 19568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 7454 35.90 - 71.81: 584 71.81 - 107.71: 17 107.71 - 143.62: 3 143.62 - 179.52: 4 Dihedral angle restraints: 8062 sinusoidal: 4145 harmonic: 3917 Sorted by residual: dihedral pdb=" C4' DA J 30 " pdb=" C3' DA J 30 " pdb=" O3' DA J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 39.52 -179.52 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 25 " pdb=" C3' DG J 25 " pdb=" O3' DG J 25 " pdb=" P DC J 26 " ideal model delta sinusoidal sigma weight residual 220.00 41.59 178.41 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 31 " pdb=" C3' DA J 31 " pdb=" O3' DA J 31 " pdb=" P DA J 32 " ideal model delta sinusoidal sigma weight residual -140.00 38.10 -178.10 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1624 0.039 - 0.079: 430 0.079 - 0.118: 115 0.118 - 0.157: 24 0.157 - 0.196: 2 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA LYS E 168 " pdb=" N LYS E 168 " pdb=" C LYS E 168 " pdb=" CB LYS E 168 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA TRP E 166 " pdb=" N TRP E 166 " pdb=" C TRP E 166 " pdb=" CB TRP E 166 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA VAL B 303 " pdb=" N VAL B 303 " pdb=" C VAL B 303 " pdb=" CB VAL B 303 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2192 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 50 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO B 51 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 291 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO E 292 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 160 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LYS E 160 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS E 160 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS E 161 " 0.010 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1663 2.75 - 3.29: 12870 3.29 - 3.82: 25087 3.82 - 4.36: 29445 4.36 - 4.90: 47320 Nonbonded interactions: 116385 Sorted by model distance: nonbonded pdb=" OH TYR E 223 " pdb=" N2 DG G 27 " model vdw 2.211 3.120 nonbonded pdb=" NH2 ARG E 124 " pdb=" OE1 GLU E 281 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR B 126 " pdb=" O4 DT H 29 " model vdw 2.253 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OP1 DT H 23 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR E 92 " pdb=" OP2 DC G 24 " model vdw 2.254 3.040 ... (remaining 116380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and resid 1 through 92) } ncs_group { reference = (chain 'B' and resid 20 through 282) selection = (chain 'C' and resid 20 through 282) selection = (chain 'E' and resid 20 through 282) selection = (chain 'F' and resid 20 through 282) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.200 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14026 Z= 0.194 Angle : 0.598 9.109 19573 Z= 0.341 Chirality : 0.039 0.196 2195 Planarity : 0.004 0.049 2042 Dihedral : 20.880 179.521 5552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.23), residues: 1347 helix: 1.66 (0.20), residues: 635 sheet: -0.29 (0.37), residues: 214 loop : -0.85 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 166 HIS 0.012 0.001 HIS B 198 PHE 0.017 0.002 PHE A 35 TYR 0.015 0.002 TYR E 162 ARG 0.007 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.14203 ( 655) hydrogen bonds : angle 6.27044 ( 1812) covalent geometry : bond 0.00434 (14026) covalent geometry : angle 0.59819 (19573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 1.195 Fit side-chains REVERT: A 3 MET cc_start: 0.7611 (ttt) cc_final: 0.6837 (ttt) REVERT: B 175 ASP cc_start: 0.7927 (t0) cc_final: 0.7550 (t70) REVERT: B 275 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (m-30) REVERT: B 289 GLU cc_start: 0.7826 (tp30) cc_final: 0.7613 (tp30) REVERT: C 162 TYR cc_start: 0.8341 (m-80) cc_final: 0.7963 (m-80) REVERT: C 233 ILE cc_start: 0.7577 (mt) cc_final: 0.7260 (mt) REVERT: C 274 LYS cc_start: 0.8113 (tppt) cc_final: 0.7883 (tptp) REVERT: E 72 GLU cc_start: 0.7249 (tp30) cc_final: 0.6892 (mm-30) REVERT: E 76 ASP cc_start: 0.6861 (m-30) cc_final: 0.6636 (m-30) REVERT: E 154 LYS cc_start: 0.7294 (tppp) cc_final: 0.6566 (tppt) REVERT: E 172 ASN cc_start: 0.8074 (t0) cc_final: 0.7646 (t0) REVERT: E 175 ASP cc_start: 0.7559 (t70) cc_final: 0.7091 (m-30) REVERT: E 193 LEU cc_start: 0.8391 (tp) cc_final: 0.8148 (tp) REVERT: E 272 MET cc_start: 0.7782 (mtt) cc_final: 0.7550 (mtp) REVERT: F 101 SER cc_start: 0.8939 (t) cc_final: 0.8702 (p) REVERT: F 275 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.3018 time to fit residues: 121.4081 Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN C 33 ASN E 183 ASN F 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116843 restraints weight = 17020.422| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.35 r_work: 0.3276 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14026 Z= 0.197 Angle : 0.608 6.664 19573 Z= 0.341 Chirality : 0.042 0.166 2195 Planarity : 0.004 0.048 2042 Dihedral : 24.231 177.874 3008 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.44 % Allowed : 8.63 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.23), residues: 1347 helix: 1.72 (0.20), residues: 641 sheet: -0.46 (0.36), residues: 216 loop : -0.82 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 296 HIS 0.009 0.001 HIS E 29 PHE 0.009 0.001 PHE E 239 TYR 0.013 0.002 TYR E 223 ARG 0.006 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 655) hydrogen bonds : angle 4.30360 ( 1812) covalent geometry : bond 0.00454 (14026) covalent geometry : angle 0.60776 (19573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 1.295 Fit side-chains REVERT: A 3 MET cc_start: 0.7950 (ttt) cc_final: 0.7283 (ttt) REVERT: A 45 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7122 (mtp85) REVERT: A 73 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7541 (tp30) REVERT: B 138 LEU cc_start: 0.8570 (mp) cc_final: 0.8320 (tp) REVERT: B 289 GLU cc_start: 0.8211 (tp30) cc_final: 0.7772 (tp30) REVERT: C 156 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7261 (ptt90) REVERT: C 162 TYR cc_start: 0.8303 (m-80) cc_final: 0.7961 (m-80) REVERT: C 253 GLN cc_start: 0.8033 (tt0) cc_final: 0.7816 (mt0) REVERT: D 51 MET cc_start: 0.8452 (ptt) cc_final: 0.8227 (ptt) REVERT: D 78 SER cc_start: 0.8236 (m) cc_final: 0.7933 (t) REVERT: E 72 GLU cc_start: 0.7623 (tp30) cc_final: 0.6611 (tp30) REVERT: E 76 ASP cc_start: 0.7048 (m-30) cc_final: 0.6555 (m-30) REVERT: E 155 TYR cc_start: 0.7303 (m-10) cc_final: 0.6990 (m-80) REVERT: E 172 ASN cc_start: 0.7957 (t0) cc_final: 0.7628 (t0) REVERT: F 101 SER cc_start: 0.9157 (t) cc_final: 0.8808 (p) REVERT: F 275 ASP cc_start: 0.8236 (m-30) cc_final: 0.7825 (m-30) outliers start: 16 outliers final: 10 residues processed: 214 average time/residue: 0.3028 time to fit residues: 90.5476 Evaluate side-chains 190 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 237 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 104 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118262 restraints weight = 18925.899| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.45 r_work: 0.3260 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14026 Z= 0.165 Angle : 0.557 6.490 19573 Z= 0.314 Chirality : 0.040 0.223 2195 Planarity : 0.004 0.047 2042 Dihedral : 24.309 177.168 3008 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.89 % Allowed : 11.78 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.23), residues: 1347 helix: 1.85 (0.20), residues: 641 sheet: -0.47 (0.36), residues: 210 loop : -0.83 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 296 HIS 0.008 0.001 HIS E 29 PHE 0.010 0.001 PHE A 89 TYR 0.020 0.001 TYR E 223 ARG 0.007 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 655) hydrogen bonds : angle 3.98560 ( 1812) covalent geometry : bond 0.00376 (14026) covalent geometry : angle 0.55744 (19573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 3 MET cc_start: 0.7781 (ttt) cc_final: 0.7039 (ttt) REVERT: A 45 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7233 (mtp85) REVERT: A 73 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7625 (tp30) REVERT: B 138 LEU cc_start: 0.8604 (mp) cc_final: 0.8377 (tp) REVERT: B 281 GLU cc_start: 0.8137 (mp0) cc_final: 0.7450 (mp0) REVERT: C 49 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7492 (mtp180) REVERT: C 156 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7173 (ptt90) REVERT: C 162 TYR cc_start: 0.8206 (m-80) cc_final: 0.7805 (m-80) REVERT: C 253 GLN cc_start: 0.7974 (tt0) cc_final: 0.7683 (mt0) REVERT: C 300 GLU cc_start: 0.7934 (tp30) cc_final: 0.7629 (tp30) REVERT: D 58 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (ttt) REVERT: D 78 SER cc_start: 0.8207 (m) cc_final: 0.7847 (t) REVERT: E 72 GLU cc_start: 0.7580 (tp30) cc_final: 0.6683 (tm-30) REVERT: E 76 ASP cc_start: 0.7233 (m-30) cc_final: 0.6631 (m-30) REVERT: E 155 TYR cc_start: 0.7322 (m-10) cc_final: 0.7008 (m-80) REVERT: E 172 ASN cc_start: 0.7997 (t0) cc_final: 0.7593 (t0) REVERT: E 193 LEU cc_start: 0.8207 (tp) cc_final: 0.7763 (tp) REVERT: F 101 SER cc_start: 0.9164 (t) cc_final: 0.8763 (p) REVERT: F 104 PHE cc_start: 0.8624 (m-10) cc_final: 0.8388 (m-10) outliers start: 21 outliers final: 15 residues processed: 212 average time/residue: 0.2955 time to fit residues: 88.0506 Evaluate side-chains 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.174300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110221 restraints weight = 18338.362| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.53 r_work: 0.3163 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 14026 Z= 0.283 Angle : 0.649 6.541 19573 Z= 0.358 Chirality : 0.044 0.185 2195 Planarity : 0.005 0.053 2042 Dihedral : 24.628 176.087 3008 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.52 % Allowed : 12.68 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.23), residues: 1347 helix: 1.56 (0.20), residues: 639 sheet: -0.59 (0.36), residues: 208 loop : -1.04 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 166 HIS 0.009 0.002 HIS E 29 PHE 0.013 0.002 PHE E 239 TYR 0.019 0.002 TYR F 26 ARG 0.008 0.001 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 655) hydrogen bonds : angle 4.28433 ( 1812) covalent geometry : bond 0.00666 (14026) covalent geometry : angle 0.64863 (19573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.192 Fit side-chains REVERT: A 45 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7375 (mtp85) REVERT: B 130 PHE cc_start: 0.7334 (m-80) cc_final: 0.6851 (m-80) REVERT: C 49 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7845 (mtp85) REVERT: E 72 GLU cc_start: 0.7739 (tp30) cc_final: 0.6890 (tm-30) REVERT: E 76 ASP cc_start: 0.7313 (m-30) cc_final: 0.6608 (m-30) REVERT: E 155 TYR cc_start: 0.7612 (m-10) cc_final: 0.7284 (m-80) REVERT: E 172 ASN cc_start: 0.8034 (t0) cc_final: 0.7656 (t0) REVERT: F 100 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7711 (mmt90) REVERT: F 101 SER cc_start: 0.9134 (t) cc_final: 0.8747 (p) REVERT: F 270 LYS cc_start: 0.8268 (mttp) cc_final: 0.7886 (mtpp) REVERT: F 275 ASP cc_start: 0.8255 (m-30) cc_final: 0.8010 (m-30) outliers start: 28 outliers final: 20 residues processed: 201 average time/residue: 0.2871 time to fit residues: 80.1337 Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.178998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116517 restraints weight = 18554.730| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.42 r_work: 0.3250 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14026 Z= 0.156 Angle : 0.557 6.432 19573 Z= 0.314 Chirality : 0.040 0.175 2195 Planarity : 0.004 0.047 2042 Dihedral : 24.527 175.708 3008 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.16 % Allowed : 14.48 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.23), residues: 1347 helix: 1.84 (0.20), residues: 640 sheet: -0.56 (0.37), residues: 198 loop : -0.95 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 166 HIS 0.005 0.001 HIS E 29 PHE 0.014 0.001 PHE C 239 TYR 0.012 0.001 TYR F 229 ARG 0.006 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 655) hydrogen bonds : angle 3.93424 ( 1812) covalent geometry : bond 0.00356 (14026) covalent geometry : angle 0.55685 (19573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.282 Fit side-chains REVERT: A 3 MET cc_start: 0.7939 (ttt) cc_final: 0.7463 (ttt) REVERT: A 45 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7221 (mtp85) REVERT: B 130 PHE cc_start: 0.6987 (m-80) cc_final: 0.6483 (m-80) REVERT: C 125 MET cc_start: 0.7234 (mtt) cc_final: 0.7021 (mtp) REVERT: D 51 MET cc_start: 0.8603 (ptt) cc_final: 0.8170 (ptt) REVERT: D 78 SER cc_start: 0.8308 (m) cc_final: 0.7933 (t) REVERT: E 72 GLU cc_start: 0.7724 (tp30) cc_final: 0.7487 (tm-30) REVERT: E 155 TYR cc_start: 0.7300 (m-10) cc_final: 0.6967 (m-80) REVERT: E 172 ASN cc_start: 0.8038 (t0) cc_final: 0.7631 (t0) REVERT: F 101 SER cc_start: 0.9110 (t) cc_final: 0.8701 (p) outliers start: 24 outliers final: 13 residues processed: 202 average time/residue: 0.2897 time to fit residues: 81.9896 Evaluate side-chains 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 141 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114188 restraints weight = 27592.922| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.01 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14026 Z= 0.196 Angle : 0.584 6.363 19573 Z= 0.325 Chirality : 0.041 0.193 2195 Planarity : 0.004 0.047 2042 Dihedral : 24.653 175.741 3008 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.16 % Allowed : 15.74 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.23), residues: 1347 helix: 1.82 (0.20), residues: 639 sheet: -0.65 (0.38), residues: 195 loop : -0.93 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 83 HIS 0.007 0.001 HIS E 29 PHE 0.012 0.001 PHE C 239 TYR 0.012 0.002 TYR B 309 ARG 0.005 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 655) hydrogen bonds : angle 3.99685 ( 1812) covalent geometry : bond 0.00460 (14026) covalent geometry : angle 0.58351 (19573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.375 Fit side-chains REVERT: A 25 GLU cc_start: 0.8487 (tt0) cc_final: 0.8224 (tt0) REVERT: A 45 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.7322 (mtp85) REVERT: B 130 PHE cc_start: 0.6967 (m-80) cc_final: 0.6481 (m-80) REVERT: C 49 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7642 (mtp180) REVERT: C 140 MET cc_start: 0.7122 (mmm) cc_final: 0.6823 (mmm) REVERT: C 156 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7175 (ptt90) REVERT: D 78 SER cc_start: 0.8299 (m) cc_final: 0.7902 (t) REVERT: E 172 ASN cc_start: 0.7980 (t0) cc_final: 0.7549 (t0) REVERT: E 193 LEU cc_start: 0.8422 (tp) cc_final: 0.8215 (tp) REVERT: E 246 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 276 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7009 (mt) REVERT: F 101 SER cc_start: 0.9166 (t) cc_final: 0.8699 (p) outliers start: 24 outliers final: 18 residues processed: 197 average time/residue: 0.2937 time to fit residues: 81.4982 Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 0.0000 chunk 106 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.180867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119260 restraints weight = 21972.379| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.63 r_work: 0.3251 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14026 Z= 0.143 Angle : 0.541 6.386 19573 Z= 0.306 Chirality : 0.039 0.168 2195 Planarity : 0.004 0.048 2042 Dihedral : 24.496 175.306 3008 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 15.74 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.23), residues: 1347 helix: 1.97 (0.20), residues: 640 sheet: -0.59 (0.37), residues: 200 loop : -0.88 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 PHE 0.014 0.001 PHE A 89 TYR 0.011 0.001 TYR F 126 ARG 0.008 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 655) hydrogen bonds : angle 3.76247 ( 1812) covalent geometry : bond 0.00319 (14026) covalent geometry : angle 0.54145 (19573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.416 Fit side-chains REVERT: A 45 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7289 (mtp85) REVERT: B 130 PHE cc_start: 0.6915 (m-80) cc_final: 0.6428 (m-80) REVERT: C 140 MET cc_start: 0.7120 (mmm) cc_final: 0.6869 (mmm) REVERT: D 78 SER cc_start: 0.8332 (m) cc_final: 0.7928 (t) REVERT: E 172 ASN cc_start: 0.7993 (t0) cc_final: 0.7629 (t0) REVERT: E 193 LEU cc_start: 0.8308 (tp) cc_final: 0.7997 (tp) REVERT: F 101 SER cc_start: 0.9132 (t) cc_final: 0.8675 (p) outliers start: 23 outliers final: 13 residues processed: 205 average time/residue: 0.2782 time to fit residues: 80.8406 Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 83 optimal weight: 3.9990 chunk 145 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.174727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112288 restraints weight = 15954.267| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.39 r_work: 0.3185 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14026 Z= 0.271 Angle : 0.636 7.573 19573 Z= 0.350 Chirality : 0.044 0.186 2195 Planarity : 0.005 0.048 2042 Dihedral : 24.660 176.402 3008 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.44 % Allowed : 17.72 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.23), residues: 1347 helix: 1.69 (0.20), residues: 639 sheet: -0.78 (0.37), residues: 197 loop : -1.04 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 296 HIS 0.007 0.001 HIS E 29 PHE 0.014 0.002 PHE C 239 TYR 0.019 0.002 TYR F 26 ARG 0.005 0.000 ARG C 152 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 655) hydrogen bonds : angle 4.08425 ( 1812) covalent geometry : bond 0.00643 (14026) covalent geometry : angle 0.63571 (19573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.227 Fit side-chains REVERT: A 45 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7327 (mtp85) REVERT: B 130 PHE cc_start: 0.7033 (m-80) cc_final: 0.6544 (m-80) REVERT: B 166 TRP cc_start: 0.8335 (t-100) cc_final: 0.8123 (t60) REVERT: C 140 MET cc_start: 0.7190 (mmm) cc_final: 0.6921 (mmm) REVERT: C 156 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7198 (ptt90) REVERT: E 172 ASN cc_start: 0.8002 (t0) cc_final: 0.7615 (t0) REVERT: E 193 LEU cc_start: 0.8585 (tp) cc_final: 0.8194 (tp) REVERT: E 246 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 272 MET cc_start: 0.8288 (ttm) cc_final: 0.7827 (mtt) REVERT: F 101 SER cc_start: 0.9135 (t) cc_final: 0.8666 (p) REVERT: F 107 LYS cc_start: 0.9019 (tppt) cc_final: 0.8728 (tptp) REVERT: F 270 LYS cc_start: 0.8183 (mttp) cc_final: 0.7791 (mtpp) outliers start: 16 outliers final: 15 residues processed: 180 average time/residue: 0.2996 time to fit residues: 75.3522 Evaluate side-chains 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.178841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116304 restraints weight = 25454.779| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.89 r_work: 0.3189 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14026 Z= 0.154 Angle : 0.560 7.852 19573 Z= 0.313 Chirality : 0.040 0.159 2195 Planarity : 0.004 0.061 2042 Dihedral : 24.527 176.004 3008 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.35 % Allowed : 17.81 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.23), residues: 1347 helix: 1.87 (0.20), residues: 640 sheet: -0.70 (0.36), residues: 200 loop : -0.91 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 296 HIS 0.005 0.001 HIS E 29 PHE 0.015 0.001 PHE A 89 TYR 0.014 0.001 TYR C 194 ARG 0.008 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 655) hydrogen bonds : angle 3.86294 ( 1812) covalent geometry : bond 0.00353 (14026) covalent geometry : angle 0.56032 (19573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.350 Fit side-chains REVERT: A 3 MET cc_start: 0.8043 (ttt) cc_final: 0.7649 (ttt) REVERT: A 45 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7413 (mtp85) REVERT: B 130 PHE cc_start: 0.6788 (m-80) cc_final: 0.6290 (m-80) REVERT: C 140 MET cc_start: 0.7143 (mmm) cc_final: 0.6850 (mmm) REVERT: C 156 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7219 (ptt90) REVERT: D 78 SER cc_start: 0.8241 (m) cc_final: 0.7858 (t) REVERT: E 172 ASN cc_start: 0.8052 (t0) cc_final: 0.7658 (t0) REVERT: E 272 MET cc_start: 0.8207 (ttm) cc_final: 0.7822 (mtt) REVERT: F 101 SER cc_start: 0.9128 (t) cc_final: 0.8638 (p) REVERT: F 275 ASP cc_start: 0.8261 (m-30) cc_final: 0.8022 (m-30) outliers start: 15 outliers final: 14 residues processed: 182 average time/residue: 0.3189 time to fit residues: 80.8695 Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.178254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116690 restraints weight = 18904.270| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.42 r_work: 0.3229 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14026 Z= 0.169 Angle : 0.573 7.865 19573 Z= 0.318 Chirality : 0.040 0.140 2195 Planarity : 0.004 0.073 2042 Dihedral : 24.492 176.090 3008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.44 % Allowed : 17.63 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.23), residues: 1347 helix: 1.88 (0.20), residues: 640 sheet: -0.64 (0.36), residues: 200 loop : -0.87 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 PHE 0.014 0.001 PHE A 89 TYR 0.023 0.001 TYR F 126 ARG 0.010 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 655) hydrogen bonds : angle 3.86508 ( 1812) covalent geometry : bond 0.00394 (14026) covalent geometry : angle 0.57340 (19573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.772 Fit side-chains REVERT: A 45 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7364 (mtp85) REVERT: B 130 PHE cc_start: 0.6861 (m-80) cc_final: 0.6437 (m-80) REVERT: B 166 TRP cc_start: 0.8317 (t-100) cc_final: 0.8102 (t60) REVERT: C 140 MET cc_start: 0.7124 (mmm) cc_final: 0.6819 (mmm) REVERT: C 156 ARG cc_start: 0.7463 (mtm110) cc_final: 0.7223 (ptt90) REVERT: D 78 SER cc_start: 0.8282 (m) cc_final: 0.7870 (t) REVERT: E 172 ASN cc_start: 0.8139 (t0) cc_final: 0.7758 (t0) REVERT: E 272 MET cc_start: 0.8205 (ttm) cc_final: 0.7763 (mtt) REVERT: F 101 SER cc_start: 0.9114 (t) cc_final: 0.8637 (p) REVERT: F 270 LYS cc_start: 0.8082 (mttp) cc_final: 0.7686 (mtpp) REVERT: F 275 ASP cc_start: 0.8239 (m-30) cc_final: 0.7923 (m-30) outliers start: 16 outliers final: 15 residues processed: 182 average time/residue: 0.4686 time to fit residues: 123.8139 Evaluate side-chains 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 6 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 38 optimal weight: 0.0050 chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 81 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.180930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118296 restraints weight = 20902.496| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.63 r_work: 0.3247 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14026 Z= 0.144 Angle : 0.552 8.910 19573 Z= 0.307 Chirality : 0.040 0.144 2195 Planarity : 0.004 0.068 2042 Dihedral : 24.399 176.119 3008 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.35 % Allowed : 17.63 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.23), residues: 1347 helix: 1.90 (0.20), residues: 641 sheet: -0.57 (0.36), residues: 200 loop : -0.81 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 PHE 0.014 0.001 PHE A 89 TYR 0.009 0.001 TYR F 229 ARG 0.009 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 655) hydrogen bonds : angle 3.81194 ( 1812) covalent geometry : bond 0.00325 (14026) covalent geometry : angle 0.55153 (19573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10846.37 seconds wall clock time: 188 minutes 52.04 seconds (11332.04 seconds total)