Starting phenix.real_space_refine on Sun Nov 17 13:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_29563.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_29563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_29563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_29563.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyb_29563/11_2024/8fyb_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.39, per 1000 atoms: 0.62 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 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: 5.22 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: 4.67 Time building geometry restraints manager: 3.75 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.390 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- 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= 0.276 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 *********************** 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 : 1.319 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: 0.3321 time to fit residues: 134.3942 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 : 1.364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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= 0.286 Angle : 0.608 6.663 19573 Z= 0.341 Chirality : 0.042 0.166 2195 Planarity : 0.004 0.047 2042 Dihedral : 24.232 177.877 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 *********************** 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 : 1.243 Fit side-chains REVERT: A 3 MET cc_start: 0.7662 (ttt) cc_final: 0.6817 (ttt) REVERT: A 45 ARG cc_start: 0.7005 (mmm-85) cc_final: 0.6678 (mtp85) REVERT: A 73 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7107 (tp30) REVERT: B 289 GLU cc_start: 0.8025 (tp30) cc_final: 0.7656 (tp30) REVERT: C 156 ARG cc_start: 0.7426 (mtm110) cc_final: 0.7168 (ptt90) REVERT: C 162 TYR cc_start: 0.8383 (m-80) cc_final: 0.8055 (m-80) REVERT: C 253 GLN cc_start: 0.7741 (tt0) cc_final: 0.7534 (mt0) REVERT: D 51 MET cc_start: 0.8397 (ptt) cc_final: 0.8157 (ptt) REVERT: D 78 SER cc_start: 0.8131 (m) cc_final: 0.7858 (t) REVERT: E 72 GLU cc_start: 0.7293 (tp30) cc_final: 0.6297 (tp30) REVERT: E 76 ASP cc_start: 0.6784 (m-30) cc_final: 0.6346 (m-30) REVERT: E 155 TYR cc_start: 0.7276 (m-10) cc_final: 0.6961 (m-80) REVERT: E 172 ASN cc_start: 0.7989 (t0) cc_final: 0.7679 (t0) REVERT: F 101 SER cc_start: 0.9013 (t) cc_final: 0.8715 (p) REVERT: F 275 ASP cc_start: 0.8013 (m-30) cc_final: 0.7636 (m-30) outliers start: 16 outliers final: 10 residues processed: 214 average time/residue: 0.2982 time to fit residues: 89.1932 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 : 1.208 ------------------------------------------------------------------------------- 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 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 0.0470 chunk 106 optimal weight: 0.0470 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2326 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= 0.203 Angle : 0.547 6.513 19573 Z= 0.309 Chirality : 0.040 0.174 2195 Planarity : 0.004 0.046 2042 Dihedral : 24.285 177.274 3008 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.80 % Allowed : 11.69 % Favored : 86.51 % 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: 0.80 (0.23), residues: 1347 helix: 1.92 (0.20), residues: 639 sheet: -0.39 (0.37), residues: 198 loop : -0.87 (0.25), residues: 510 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 0.023 0.001 TYR E 223 ARG 0.007 0.001 ARG E 49 *********************** 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 224 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7174 (mmm-85) cc_final: 0.6798 (mtp85) REVERT: A 73 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7158 (tp30) REVERT: B 281 GLU cc_start: 0.7920 (mp0) cc_final: 0.7447 (mp0) REVERT: C 156 ARG cc_start: 0.7308 (mtm110) cc_final: 0.7040 (ptt90) REVERT: C 253 GLN cc_start: 0.7629 (tt0) cc_final: 0.7333 (mt0) REVERT: D 58 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7765 (ttt) REVERT: D 78 SER cc_start: 0.8170 (m) cc_final: 0.7903 (t) REVERT: E 72 GLU cc_start: 0.7363 (tp30) cc_final: 0.6509 (tm-30) REVERT: E 76 ASP cc_start: 0.6963 (m-30) cc_final: 0.6412 (m-30) REVERT: E 172 ASN cc_start: 0.8053 (t0) cc_final: 0.7679 (t0) REVERT: E 193 LEU cc_start: 0.8163 (tp) cc_final: 0.7739 (tp) REVERT: F 101 SER cc_start: 0.9034 (t) cc_final: 0.8716 (p) REVERT: F 104 PHE cc_start: 0.8436 (m-10) cc_final: 0.8180 (m-10) outliers start: 20 outliers final: 14 residues processed: 215 average time/residue: 0.2915 time to fit residues: 88.4558 Evaluate side-chains 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14026 Z= 0.245 Angle : 0.557 6.428 19573 Z= 0.314 Chirality : 0.040 0.171 2195 Planarity : 0.004 0.047 2042 Dihedral : 24.344 177.010 3008 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.25 % Allowed : 12.05 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.23), residues: 1347 helix: 1.96 (0.20), residues: 641 sheet: -0.34 (0.38), residues: 198 loop : -0.91 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 166 HIS 0.007 0.001 HIS E 29 PHE 0.010 0.001 PHE A 89 TYR 0.012 0.001 TYR F 229 ARG 0.007 0.000 ARG B 116 *********************** 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 223 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.283 Fit side-chains REVERT: A 45 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6820 (mtp85) REVERT: A 73 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7174 (tp30) REVERT: B 281 GLU cc_start: 0.8002 (mp0) cc_final: 0.7364 (mp0) REVERT: C 250 ASP cc_start: 0.7594 (t70) cc_final: 0.7051 (t70) REVERT: D 51 MET cc_start: 0.8603 (ptt) cc_final: 0.8183 (ptt) REVERT: D 58 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: D 78 SER cc_start: 0.8176 (m) cc_final: 0.7874 (t) REVERT: E 72 GLU cc_start: 0.7369 (tp30) cc_final: 0.6464 (tm-30) REVERT: E 76 ASP cc_start: 0.6967 (m-30) cc_final: 0.6391 (m-30) REVERT: E 124 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.6610 (ttp-170) REVERT: E 155 TYR cc_start: 0.7517 (m-10) cc_final: 0.7233 (m-80) REVERT: E 172 ASN cc_start: 0.8083 (t0) cc_final: 0.7705 (t0) REVERT: F 101 SER cc_start: 0.9006 (t) cc_final: 0.8672 (p) REVERT: F 104 PHE cc_start: 0.8481 (m-10) cc_final: 0.8267 (m-10) outliers start: 25 outliers final: 17 residues processed: 211 average time/residue: 0.2935 time to fit residues: 86.7498 Evaluate side-chains 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 147 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 C residue 254 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain E residue 50 ILE 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 18 VAL Chi-restraints excluded: chain F residue 35 VAL 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 117 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2770 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= 0.210 Angle : 0.548 6.454 19573 Z= 0.309 Chirality : 0.040 0.207 2195 Planarity : 0.004 0.059 2042 Dihedral : 24.376 176.048 3008 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 13.49 % Favored : 84.44 % 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: 0.86 (0.23), residues: 1347 helix: 2.02 (0.20), residues: 642 sheet: -0.34 (0.37), residues: 197 loop : -0.93 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 296 HIS 0.006 0.001 HIS E 29 PHE 0.011 0.001 PHE A 89 TYR 0.015 0.001 TYR B 305 ARG 0.007 0.000 ARG C 49 *********************** 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 209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.453 Fit side-chains REVERT: A 45 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6837 (mtp85) REVERT: A 73 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7131 (tp30) REVERT: B 92 TYR cc_start: 0.8158 (m-80) cc_final: 0.7857 (m-10) REVERT: C 253 GLN cc_start: 0.7880 (tt0) cc_final: 0.7587 (mt0) REVERT: D 51 MET cc_start: 0.8570 (ptt) cc_final: 0.8210 (ptt) REVERT: D 58 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7828 (ttt) REVERT: D 78 SER cc_start: 0.8189 (m) cc_final: 0.7899 (t) REVERT: E 155 TYR cc_start: 0.7396 (m-10) cc_final: 0.7122 (m-80) REVERT: E 172 ASN cc_start: 0.8073 (t0) cc_final: 0.7736 (t0) REVERT: F 100 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7157 (mtm180) REVERT: F 101 SER cc_start: 0.8996 (t) cc_final: 0.8650 (p) REVERT: F 104 PHE cc_start: 0.8489 (m-10) cc_final: 0.8266 (m-10) REVERT: F 116 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7507 (mmm-85) outliers start: 23 outliers final: 15 residues processed: 197 average time/residue: 0.2995 time to fit residues: 82.9948 Evaluate side-chains 192 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 147 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 58 MET 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 277 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2961 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= 0.215 Angle : 0.548 6.341 19573 Z= 0.307 Chirality : 0.040 0.206 2195 Planarity : 0.004 0.060 2042 Dihedral : 24.457 175.823 3008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 14.03 % Favored : 83.72 % 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: 0.95 (0.23), residues: 1347 helix: 2.09 (0.20), residues: 640 sheet: -0.36 (0.37), residues: 198 loop : -0.85 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 296 HIS 0.007 0.001 HIS E 29 PHE 0.010 0.001 PHE A 89 TYR 0.013 0.001 TYR B 309 ARG 0.005 0.000 ARG E 116 *********************** 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 211 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.339 Fit side-chains REVERT: A 45 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6836 (mtp85) REVERT: B 92 TYR cc_start: 0.8164 (m-80) cc_final: 0.7848 (m-10) REVERT: B 130 PHE cc_start: 0.7255 (m-80) cc_final: 0.6811 (m-80) REVERT: B 272 MET cc_start: 0.7492 (mtp) cc_final: 0.7239 (mtp) REVERT: C 253 GLN cc_start: 0.7890 (tt0) cc_final: 0.7539 (mt0) REVERT: D 51 MET cc_start: 0.8582 (ptt) cc_final: 0.8265 (ptt) REVERT: D 58 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7913 (ttt) REVERT: D 78 SER cc_start: 0.8213 (m) cc_final: 0.7929 (t) REVERT: E 155 TYR cc_start: 0.7393 (m-10) cc_final: 0.7154 (m-80) REVERT: E 172 ASN cc_start: 0.8096 (t0) cc_final: 0.7771 (t0) REVERT: E 246 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7023 (tm-30) REVERT: E 247 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: F 36 ASP cc_start: 0.7429 (m-30) cc_final: 0.7099 (m-30) REVERT: F 100 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7143 (mtm180) REVERT: F 101 SER cc_start: 0.9009 (t) cc_final: 0.8628 (p) REVERT: F 104 PHE cc_start: 0.8516 (m-10) cc_final: 0.8298 (m-10) outliers start: 25 outliers final: 14 residues processed: 198 average time/residue: 0.2851 time to fit residues: 80.1751 Evaluate side-chains 189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 147 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 247 GLU 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 136 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 79 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3137 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= 0.204 Angle : 0.536 6.381 19573 Z= 0.302 Chirality : 0.039 0.139 2195 Planarity : 0.004 0.060 2042 Dihedral : 24.413 176.015 3008 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 13.94 % Favored : 83.90 % 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: 0.99 (0.23), residues: 1347 helix: 2.12 (0.20), residues: 641 sheet: -0.37 (0.37), residues: 198 loop : -0.82 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 296 HIS 0.008 0.001 HIS E 29 PHE 0.011 0.001 PHE E 263 TYR 0.012 0.001 TYR B 309 ARG 0.008 0.000 ARG B 116 *********************** 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 205 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.505 Fit side-chains REVERT: A 45 ARG cc_start: 0.7176 (mmm-85) cc_final: 0.6842 (mtp85) REVERT: B 130 PHE cc_start: 0.7161 (m-80) cc_final: 0.6697 (m-80) REVERT: C 253 GLN cc_start: 0.7865 (tt0) cc_final: 0.7483 (mt0) REVERT: D 51 MET cc_start: 0.8585 (ptt) cc_final: 0.8288 (ptt) REVERT: D 58 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7816 (ttt) REVERT: D 78 SER cc_start: 0.8309 (m) cc_final: 0.7960 (t) REVERT: E 155 TYR cc_start: 0.7333 (m-10) cc_final: 0.7100 (m-80) REVERT: E 172 ASN cc_start: 0.8254 (t0) cc_final: 0.7897 (t0) REVERT: F 101 SER cc_start: 0.9000 (t) cc_final: 0.8608 (p) REVERT: F 104 PHE cc_start: 0.8534 (m-10) cc_final: 0.8317 (m-10) REVERT: F 116 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7427 (mmm-85) outliers start: 24 outliers final: 13 residues processed: 192 average time/residue: 0.2759 time to fit residues: 75.3838 Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR 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 147 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 D residue 58 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 0.0040 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3294 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= 0.204 Angle : 0.537 6.738 19573 Z= 0.301 Chirality : 0.039 0.139 2195 Planarity : 0.004 0.059 2042 Dihedral : 24.394 176.208 3008 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.62 % Allowed : 14.84 % Favored : 83.54 % 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: 0.98 (0.23), residues: 1347 helix: 2.10 (0.20), residues: 641 sheet: -0.37 (0.36), residues: 198 loop : -0.81 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 83 HIS 0.007 0.001 HIS E 29 PHE 0.010 0.001 PHE A 89 TYR 0.013 0.001 TYR F 126 ARG 0.006 0.000 ARG C 124 *********************** 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 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.318 Fit side-chains REVERT: A 45 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6879 (mtp85) REVERT: B 130 PHE cc_start: 0.7176 (m-80) cc_final: 0.6716 (m-80) REVERT: C 253 GLN cc_start: 0.7875 (tt0) cc_final: 0.7453 (mt0) REVERT: D 58 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7804 (ttt) REVERT: D 78 SER cc_start: 0.8328 (m) cc_final: 0.7982 (t) REVERT: E 172 ASN cc_start: 0.8280 (t0) cc_final: 0.7899 (t0) REVERT: F 36 ASP cc_start: 0.7420 (m-30) cc_final: 0.7088 (m-30) REVERT: F 101 SER cc_start: 0.9026 (t) cc_final: 0.8614 (p) REVERT: F 104 PHE cc_start: 0.8554 (m-10) cc_final: 0.8348 (m-10) outliers start: 18 outliers final: 14 residues processed: 179 average time/residue: 0.2962 time to fit residues: 74.7623 Evaluate side-chains 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 147 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 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 247 GLU 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 237 ILE 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 134 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.005 0.046 14026 Z= 0.349 Angle : 0.600 7.173 19573 Z= 0.330 Chirality : 0.042 0.277 2195 Planarity : 0.004 0.056 2042 Dihedral : 24.577 176.569 3008 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.44 % Allowed : 14.93 % Favored : 83.63 % 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: 0.72 (0.23), residues: 1347 helix: 1.89 (0.21), residues: 639 sheet: -0.51 (0.36), residues: 200 loop : -0.93 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 296 HIS 0.007 0.001 HIS E 29 PHE 0.013 0.001 PHE C 239 TYR 0.015 0.002 TYR F 26 ARG 0.009 0.001 ARG C 144 *********************** 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 187 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.345 Fit side-chains REVERT: A 3 MET cc_start: 0.7954 (ttt) cc_final: 0.7367 (ttt) REVERT: A 45 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6902 (mtp85) REVERT: B 130 PHE cc_start: 0.7299 (m-80) cc_final: 0.6853 (m-80) REVERT: D 78 SER cc_start: 0.8313 (m) cc_final: 0.7979 (t) REVERT: E 172 ASN cc_start: 0.8267 (t0) cc_final: 0.7878 (t0) REVERT: F 101 SER cc_start: 0.9027 (t) cc_final: 0.8599 (p) outliers start: 16 outliers final: 10 residues processed: 177 average time/residue: 0.3017 time to fit residues: 75.0347 Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 244 GLU Chi-restraints excluded: chain C residue 251 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 145 optimal weight: 30.0000 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN D 13 GLN ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3469 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= 0.226 Angle : 0.557 7.106 19573 Z= 0.309 Chirality : 0.040 0.251 2195 Planarity : 0.004 0.058 2042 Dihedral : 24.492 176.006 3008 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.99 % Allowed : 15.83 % Favored : 83.18 % 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: 1.93 (0.20), residues: 640 sheet: -0.46 (0.36), residues: 198 loop : -0.88 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.006 0.001 HIS E 29 PHE 0.011 0.001 PHE C 239 TYR 0.023 0.001 TYR F 126 ARG 0.013 0.000 ARG C 144 ********************** 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 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 1.355 Fit side-chains REVERT: A 45 ARG cc_start: 0.7190 (mmm-85) cc_final: 0.6871 (mtp85) REVERT: B 130 PHE cc_start: 0.7217 (m-80) cc_final: 0.6779 (m-80) REVERT: D 73 GLU cc_start: 0.7558 (tp30) cc_final: 0.7358 (tp30) REVERT: D 78 SER cc_start: 0.8290 (m) cc_final: 0.7981 (t) REVERT: E 172 ASN cc_start: 0.8253 (t0) cc_final: 0.7839 (t0) REVERT: F 101 SER cc_start: 0.9010 (t) cc_final: 0.8588 (p) outliers start: 11 outliers final: 10 residues processed: 177 average time/residue: 0.3030 time to fit residues: 75.3750 Evaluate side-chains 176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 244 GLU Chi-restraints excluded: chain C residue 251 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.177835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115207 restraints weight = 18003.662| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.35 r_work: 0.3226 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3551 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= 0.290 Angle : 0.577 6.702 19573 Z= 0.319 Chirality : 0.041 0.251 2195 Planarity : 0.004 0.058 2042 Dihedral : 24.521 176.616 3008 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.08 % Allowed : 15.92 % Favored : 83.00 % 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: 0.68 (0.23), residues: 1347 helix: 1.83 (0.21), residues: 639 sheet: -0.57 (0.36), residues: 200 loop : -0.89 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS E 29 PHE 0.011 0.001 PHE C 239 TYR 0.012 0.001 TYR B 309 ARG 0.013 0.000 ARG C 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.11 seconds wall clock time: 57 minutes 54.37 seconds (3474.37 seconds total)