Starting phenix.real_space_refine on Tue Jul 29 23:28:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.map" model { file = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fya_29562/07_2025/8fya_29562.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 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 611 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 57 5.49 5 S 31 5.16 5 C 7056 2.51 5 N 2060 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 11433 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" 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: "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: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2388 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 1 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: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Time building chain proxies: 7.42, per 1000 atoms: 0.65 Number of scatterers: 11433 At special positions: 0 Unit cell: (93.66, 90.315, 142.72, 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 31 16.00 P 57 15.00 O 2229 8.00 N 2060 7.00 C 7056 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 51.2% alpha, 15.4% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.823A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 67 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: 3.982A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.872A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.536A 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 265 removed outlier: 4.343A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 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: 3.871A 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 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.517A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (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 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.722A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.526A 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 removed outlier: 3.507A pdb=" N LEU C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.539A 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 49 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' 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: 3.999A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.581A pdb=" N ARG E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.806A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.451A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.648A 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 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.881A 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 Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.758A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.868A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.798A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.461A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.105A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.901A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.287A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291 removed outlier: 7.715A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 7.598A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3360 1.34 - 1.45: 2039 1.45 - 1.57: 6193 1.57 - 1.69: 114 1.69 - 1.81: 60 Bond restraints: 11766 Sorted by residual: bond pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" C4' DG G 24 " pdb=" O4' DG G 24 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 9.49e-01 bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.78e-01 bond pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.70e-02 3.46e+03 7.95e-01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 15632 1.20 - 2.41: 432 2.41 - 3.61: 87 3.61 - 4.81: 12 4.81 - 6.02: 11 Bond angle restraints: 16174 Sorted by residual: angle pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 angle pdb=" CA GLN F 87 " pdb=" CB GLN F 87 " pdb=" CG GLN F 87 " ideal model delta sigma weight residual 114.10 118.53 -4.43 2.00e+00 2.50e-01 4.90e+00 angle pdb=" C ALA E 99 " pdb=" N ARG E 100 " pdb=" CA ARG E 100 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.97e+00 angle pdb=" N VAL E 35 " pdb=" CA VAL E 35 " pdb=" C VAL E 35 " ideal model delta sigma weight residual 109.17 106.16 3.01 1.54e+00 4.22e-01 3.81e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " ideal model delta sigma weight residual 114.48 116.79 -2.31 1.19e+00 7.06e-01 3.77e+00 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6645 35.99 - 71.98: 279 71.98 - 107.97: 9 107.97 - 143.96: 0 143.96 - 179.96: 1 Dihedral angle restraints: 6934 sinusoidal: 3177 harmonic: 3757 Sorted by residual: dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual -140.00 39.96 -179.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU F 19 " pdb=" C GLU F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1317 0.037 - 0.074: 375 0.074 - 0.110: 100 0.110 - 0.147: 29 0.147 - 0.184: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR E 113 " pdb=" CA THR E 113 " pdb=" OG1 THR E 113 " pdb=" CG2 THR E 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1820 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 172 " -0.025 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 173 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 85 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 86 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " -0.009 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR A 31 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.000 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 11148 3.26 - 3.81: 20453 3.81 - 4.35: 25083 4.35 - 4.90: 41575 Nonbonded interactions: 98751 Sorted by model distance: nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" OD2 ASP E 275 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 7 " pdb=" OG SER A 57 " model vdw 2.201 3.040 nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.207 3.040 nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.213 3.040 ... (remaining 98746 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' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and resid 20 through 283) selection = (chain 'F' and resid 20 through 283) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.300 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:40.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11766 Z= 0.134 Angle : 0.511 6.016 16174 Z= 0.279 Chirality : 0.040 0.184 1823 Planarity : 0.003 0.047 1879 Dihedral : 16.989 179.956 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: 1.24 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 601 sheet: 0.05 (0.40), residues: 201 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 83 HIS 0.010 0.001 HIS B 29 PHE 0.008 0.001 PHE A 35 TYR 0.022 0.001 TYR A 31 ARG 0.008 0.000 ARG F 124 Details of bonding type rmsd hydrogen bonds : bond 0.16746 ( 621) hydrogen bonds : angle 6.58993 ( 1724) covalent geometry : bond 0.00299 (11766) covalent geometry : angle 0.51095 (16174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.205 Fit side-chains REVERT: A 58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp) REVERT: C 257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp) REVERT: F 254 LEU cc_start: 0.8294 (tt) cc_final: 0.8082 (tt) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 1.4731 time to fit residues: 388.3037 Evaluate side-chains 181 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125020 restraints weight = 12287.878| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.75 r_work: 0.3327 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11766 Z= 0.192 Angle : 0.575 7.525 16174 Z= 0.313 Chirality : 0.043 0.174 1823 Planarity : 0.004 0.038 1879 Dihedral : 18.489 176.845 2097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.81 % Allowed : 12.29 % Favored : 84.90 % 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: 1.10 (0.24), residues: 1288 helix: 2.08 (0.21), residues: 608 sheet: -0.21 (0.38), residues: 206 loop : -0.57 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.013 0.001 HIS B 29 PHE 0.014 0.001 PHE D 89 TYR 0.016 0.001 TYR A 31 ARG 0.006 0.000 ARG C 258 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 621) hydrogen bonds : angle 4.67889 ( 1724) covalent geometry : bond 0.00446 (11766) covalent geometry : angle 0.57516 (16174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 2.485 Fit side-chains REVERT: B 302 LEU cc_start: 0.8313 (mt) cc_final: 0.8070 (mm) REVERT: C 128 MET cc_start: 0.7562 (mtm) cc_final: 0.7340 (mtm) REVERT: C 257 LEU cc_start: 0.8287 (tt) cc_final: 0.7930 (tp) REVERT: D 10 ASN cc_start: 0.7399 (t0) cc_final: 0.7095 (m-40) REVERT: E 31 LYS cc_start: 0.8168 (mtpm) cc_final: 0.7695 (mttp) REVERT: E 244 GLU cc_start: 0.7685 (tt0) cc_final: 0.7363 (tt0) REVERT: E 289 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5431 (pp20) outliers start: 30 outliers final: 14 residues processed: 208 average time/residue: 1.4893 time to fit residues: 338.0926 Evaluate side-chains 184 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 308 ASN D 48 GLN E 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126301 restraints weight = 12411.045| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.79 r_work: 0.3332 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11766 Z= 0.154 Angle : 0.523 6.696 16174 Z= 0.286 Chirality : 0.041 0.164 1823 Planarity : 0.004 0.035 1879 Dihedral : 18.464 177.989 2095 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.94 % Allowed : 13.98 % Favored : 82.08 % 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: 1.23 (0.24), residues: 1288 helix: 2.24 (0.21), residues: 610 sheet: -0.20 (0.37), residues: 201 loop : -0.58 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.009 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.013 0.001 TYR D 31 ARG 0.006 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 621) hydrogen bonds : angle 4.39973 ( 1724) covalent geometry : bond 0.00351 (11766) covalent geometry : angle 0.52316 (16174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9086 (ttp) cc_final: 0.8666 (ttp) REVERT: B 302 LEU cc_start: 0.8264 (mt) cc_final: 0.7997 (mm) REVERT: C 17 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7565 (mtm-85) REVERT: C 128 MET cc_start: 0.7599 (mtm) cc_final: 0.7368 (mtm) REVERT: C 257 LEU cc_start: 0.8303 (tt) cc_final: 0.7949 (tp) REVERT: C 263 PHE cc_start: 0.7830 (m-10) cc_final: 0.7611 (m-10) REVERT: D 23 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8600 (ptm) REVERT: E 31 LYS cc_start: 0.8073 (mtpm) cc_final: 0.7725 (mtpp) REVERT: E 33 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7510 (m-40) REVERT: E 244 GLU cc_start: 0.7637 (tt0) cc_final: 0.7334 (tt0) REVERT: E 270 LYS cc_start: 0.7789 (mtpp) cc_final: 0.7532 (mtpt) REVERT: F 138 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6018 (tt) outliers start: 42 outliers final: 17 residues processed: 208 average time/residue: 1.4547 time to fit residues: 325.1251 Evaluate side-chains 199 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 97 optimal weight: 0.7980 chunk 101 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127496 restraints weight = 12342.210| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.79 r_work: 0.3354 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.135 Angle : 0.504 6.772 16174 Z= 0.276 Chirality : 0.040 0.154 1823 Planarity : 0.003 0.032 1879 Dihedral : 18.438 177.730 2095 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.94 % Allowed : 14.73 % Favored : 81.33 % 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: 1.35 (0.24), residues: 1288 helix: 2.35 (0.21), residues: 610 sheet: -0.23 (0.37), residues: 201 loop : -0.50 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.008 0.001 TYR B 194 ARG 0.005 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 621) hydrogen bonds : angle 4.24356 ( 1724) covalent geometry : bond 0.00305 (11766) covalent geometry : angle 0.50428 (16174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 2.226 Fit side-chains REVERT: A 58 MET cc_start: 0.9070 (ttp) cc_final: 0.8671 (ttp) REVERT: B 172 ASN cc_start: 0.8712 (t0) cc_final: 0.8315 (t0) REVERT: C 17 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7522 (mtm-85) REVERT: C 232 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: C 263 PHE cc_start: 0.7795 (m-10) cc_final: 0.7579 (m-10) REVERT: D 3 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7502 (ttt) REVERT: D 23 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8557 (ptm) REVERT: E 31 LYS cc_start: 0.7995 (mtpm) cc_final: 0.7684 (mttm) REVERT: E 33 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7517 (m-40) REVERT: E 244 GLU cc_start: 0.7648 (tt0) cc_final: 0.7325 (tt0) REVERT: E 270 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7571 (mtpt) REVERT: E 289 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5408 (pp20) REVERT: F 138 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6010 (tt) REVERT: F 253 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 281 GLU cc_start: 0.8584 (mp0) cc_final: 0.8317 (mp0) outliers start: 42 outliers final: 21 residues processed: 217 average time/residue: 1.7600 time to fit residues: 415.3793 Evaluate side-chains 198 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN D 10 ASN E 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126787 restraints weight = 12311.593| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.79 r_work: 0.3351 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.145 Angle : 0.512 6.287 16174 Z= 0.279 Chirality : 0.041 0.157 1823 Planarity : 0.003 0.031 1879 Dihedral : 18.490 177.668 2095 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.94 % Allowed : 16.42 % Favored : 79.64 % 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: 1.36 (0.24), residues: 1288 helix: 2.39 (0.21), residues: 609 sheet: -0.30 (0.37), residues: 202 loop : -0.49 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.014 0.001 TYR F 223 ARG 0.006 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 621) hydrogen bonds : angle 4.18475 ( 1724) covalent geometry : bond 0.00334 (11766) covalent geometry : angle 0.51239 (16174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.484 Fit side-chains REVERT: A 58 MET cc_start: 0.9085 (ttp) cc_final: 0.8662 (ttp) REVERT: B 33 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: B 172 ASN cc_start: 0.8719 (t0) cc_final: 0.8308 (t0) REVERT: B 302 LEU cc_start: 0.8243 (mt) cc_final: 0.8023 (mm) REVERT: C 17 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7520 (mtm-85) REVERT: C 232 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: D 3 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7553 (ttt) REVERT: D 23 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8526 (ptm) REVERT: E 31 LYS cc_start: 0.8052 (mtpm) cc_final: 0.7697 (mttm) REVERT: E 33 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7501 (m-40) REVERT: E 244 GLU cc_start: 0.7466 (tt0) cc_final: 0.7219 (tt0) REVERT: E 270 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7525 (mtpt) REVERT: F 72 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: F 103 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7699 (ttp-170) REVERT: F 138 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6011 (tt) REVERT: F 140 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7151 (tpp) outliers start: 42 outliers final: 22 residues processed: 201 average time/residue: 1.2231 time to fit residues: 268.2624 Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 GLN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123466 restraints weight = 12465.585| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.76 r_work: 0.3302 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11766 Z= 0.198 Angle : 0.554 6.153 16174 Z= 0.300 Chirality : 0.043 0.191 1823 Planarity : 0.004 0.032 1879 Dihedral : 18.659 177.729 2095 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.13 % Allowed : 17.17 % Favored : 78.71 % 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: 1.18 (0.24), residues: 1288 helix: 2.22 (0.21), residues: 610 sheet: -0.53 (0.35), residues: 212 loop : -0.48 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 PHE 0.012 0.001 PHE D 89 TYR 0.016 0.002 TYR F 223 ARG 0.006 0.000 ARG F 17 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 621) hydrogen bonds : angle 4.28652 ( 1724) covalent geometry : bond 0.00463 (11766) covalent geometry : angle 0.55418 (16174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.106 Fit side-chains REVERT: A 41 GLU cc_start: 0.7758 (tt0) cc_final: 0.7451 (tp30) REVERT: A 58 MET cc_start: 0.9129 (ttp) cc_final: 0.8659 (ttp) REVERT: B 33 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: B 172 ASN cc_start: 0.8788 (t0) cc_final: 0.8435 (t0) REVERT: B 302 LEU cc_start: 0.8264 (mt) cc_final: 0.8042 (mm) REVERT: C 17 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7591 (mtm-85) REVERT: C 232 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: D 3 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7816 (ttt) REVERT: D 23 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8537 (ptm) REVERT: D 35 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: E 31 LYS cc_start: 0.8138 (mtpm) cc_final: 0.7768 (mttm) REVERT: E 33 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7503 (m-40) REVERT: E 227 ASP cc_start: 0.8393 (m-30) cc_final: 0.8171 (m-30) REVERT: E 244 GLU cc_start: 0.7467 (tt0) cc_final: 0.7256 (tt0) REVERT: F 138 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6016 (tt) outliers start: 44 outliers final: 24 residues processed: 203 average time/residue: 1.1531 time to fit residues: 254.2365 Evaluate side-chains 206 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127042 restraints weight = 12481.378| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.77 r_work: 0.3350 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11766 Z= 0.134 Angle : 0.513 6.638 16174 Z= 0.279 Chirality : 0.041 0.163 1823 Planarity : 0.003 0.030 1879 Dihedral : 18.516 177.158 2095 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.47 % Allowed : 18.20 % Favored : 78.33 % 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: 1.31 (0.24), residues: 1288 helix: 2.34 (0.21), residues: 609 sheet: -0.38 (0.36), residues: 207 loop : -0.47 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.016 0.001 TYR F 223 ARG 0.006 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 621) hydrogen bonds : angle 4.16901 ( 1724) covalent geometry : bond 0.00304 (11766) covalent geometry : angle 0.51342 (16174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.247 Fit side-chains REVERT: A 58 MET cc_start: 0.9115 (ttp) cc_final: 0.8672 (ttp) REVERT: B 33 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: B 172 ASN cc_start: 0.8750 (t0) cc_final: 0.8369 (t0) REVERT: C 17 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7526 (mtm-85) REVERT: C 232 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7762 (pp20) REVERT: D 3 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7632 (ttt) REVERT: D 23 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8481 (ptm) REVERT: E 31 LYS cc_start: 0.8091 (mtpm) cc_final: 0.7859 (mtmm) REVERT: E 33 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7464 (m-40) REVERT: E 227 ASP cc_start: 0.8388 (m-30) cc_final: 0.8134 (m-30) REVERT: E 289 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5452 (pp20) REVERT: F 23 THR cc_start: 0.8514 (m) cc_final: 0.8284 (p) REVERT: F 138 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6104 (tt) outliers start: 37 outliers final: 20 residues processed: 205 average time/residue: 1.1513 time to fit residues: 256.9835 Evaluate side-chains 202 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 60 optimal weight: 0.7980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS F 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125188 restraints weight = 12479.028| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.74 r_work: 0.3321 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11766 Z= 0.178 Angle : 0.553 6.601 16174 Z= 0.297 Chirality : 0.043 0.261 1823 Planarity : 0.004 0.042 1879 Dihedral : 18.584 177.346 2095 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.94 % Allowed : 18.48 % Favored : 77.58 % 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: 1.15 (0.24), residues: 1288 helix: 2.20 (0.21), residues: 610 sheet: -0.54 (0.35), residues: 212 loop : -0.50 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.011 0.001 PHE F 263 TYR 0.017 0.001 TYR F 223 ARG 0.006 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 621) hydrogen bonds : angle 4.25909 ( 1724) covalent geometry : bond 0.00413 (11766) covalent geometry : angle 0.55270 (16174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7729 (tt0) cc_final: 0.7437 (tp30) REVERT: A 58 MET cc_start: 0.9118 (ttp) cc_final: 0.8654 (ttp) REVERT: B 33 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: B 172 ASN cc_start: 0.8770 (t0) cc_final: 0.8385 (t0) REVERT: C 17 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7553 (mtm-85) REVERT: C 126 TYR cc_start: 0.7986 (t80) cc_final: 0.7762 (t80) REVERT: C 232 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7775 (pp20) REVERT: D 23 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8512 (ptm) REVERT: D 35 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: D 65 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7443 (mt-10) REVERT: E 31 LYS cc_start: 0.8080 (mtpm) cc_final: 0.7786 (mtpp) REVERT: E 33 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7496 (m-40) REVERT: E 227 ASP cc_start: 0.8387 (m-30) cc_final: 0.8162 (m-30) REVERT: E 289 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5543 (pp20) outliers start: 42 outliers final: 25 residues processed: 202 average time/residue: 1.1822 time to fit residues: 260.0624 Evaluate side-chains 207 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125378 restraints weight = 12433.976| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.76 r_work: 0.3323 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11766 Z= 0.164 Angle : 0.549 7.019 16174 Z= 0.295 Chirality : 0.042 0.203 1823 Planarity : 0.004 0.051 1879 Dihedral : 18.577 176.991 2095 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.75 % Allowed : 18.76 % Favored : 77.49 % 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: 1.13 (0.24), residues: 1288 helix: 2.18 (0.21), residues: 610 sheet: -0.51 (0.36), residues: 212 loop : -0.52 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.016 0.001 TYR F 223 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 621) hydrogen bonds : angle 4.25049 ( 1724) covalent geometry : bond 0.00379 (11766) covalent geometry : angle 0.54884 (16174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8841 (mtp) cc_final: 0.8628 (mtp) REVERT: A 41 GLU cc_start: 0.7737 (tt0) cc_final: 0.7429 (tp30) REVERT: A 58 MET cc_start: 0.9087 (ttp) cc_final: 0.8626 (ttp) REVERT: B 33 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (m-40) REVERT: B 172 ASN cc_start: 0.8764 (t0) cc_final: 0.8376 (t0) REVERT: C 17 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7524 (mtm-85) REVERT: C 126 TYR cc_start: 0.7984 (t80) cc_final: 0.7780 (t80) REVERT: C 232 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7771 (pp20) REVERT: D 3 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7725 (ttt) REVERT: D 23 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8521 (ptm) REVERT: D 65 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7392 (mt-10) REVERT: E 31 LYS cc_start: 0.8093 (mtpm) cc_final: 0.7802 (mtpp) REVERT: E 33 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7473 (m-40) REVERT: E 227 ASP cc_start: 0.8389 (m-30) cc_final: 0.8164 (m-30) REVERT: E 289 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5556 (pp20) REVERT: F 23 THR cc_start: 0.8496 (m) cc_final: 0.8291 (p) outliers start: 40 outliers final: 25 residues processed: 203 average time/residue: 1.1951 time to fit residues: 264.8023 Evaluate side-chains 206 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126950 restraints weight = 12389.264| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.76 r_work: 0.3348 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11766 Z= 0.144 Angle : 0.548 7.738 16174 Z= 0.294 Chirality : 0.042 0.223 1823 Planarity : 0.004 0.033 1879 Dihedral : 18.520 176.755 2095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.91 % Allowed : 19.98 % Favored : 77.11 % 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: 1.19 (0.24), residues: 1288 helix: 2.21 (0.21), residues: 607 sheet: -0.36 (0.36), residues: 207 loop : -0.52 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.015 0.001 TYR F 223 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 621) hydrogen bonds : angle 4.22114 ( 1724) covalent geometry : bond 0.00329 (11766) covalent geometry : angle 0.54773 (16174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8826 (mtp) cc_final: 0.8548 (mtp) REVERT: A 58 MET cc_start: 0.9091 (ttp) cc_final: 0.8645 (ttp) REVERT: A 73 GLU cc_start: 0.7052 (tt0) cc_final: 0.6841 (tt0) REVERT: B 33 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: B 172 ASN cc_start: 0.8719 (t0) cc_final: 0.8341 (t0) REVERT: C 17 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7509 (mtm-85) REVERT: C 126 TYR cc_start: 0.8029 (t80) cc_final: 0.7803 (t80) REVERT: C 232 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7668 (pp20) REVERT: D 3 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7630 (ttt) REVERT: D 23 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8496 (ptm) REVERT: E 31 LYS cc_start: 0.8006 (mtpm) cc_final: 0.7799 (mtpp) REVERT: E 33 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: E 227 ASP cc_start: 0.8382 (m-30) cc_final: 0.8150 (m-30) REVERT: E 289 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5562 (pp20) outliers start: 31 outliers final: 24 residues processed: 194 average time/residue: 1.3181 time to fit residues: 278.6038 Evaluate side-chains 202 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128491 restraints weight = 12316.102| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.75 r_work: 0.3357 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11766 Z= 0.132 Angle : 0.541 7.602 16174 Z= 0.291 Chirality : 0.042 0.205 1823 Planarity : 0.004 0.048 1879 Dihedral : 18.427 176.523 2095 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.10 % Allowed : 19.89 % Favored : 77.02 % 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: 1.20 (0.24), residues: 1288 helix: 2.21 (0.21), residues: 607 sheet: -0.36 (0.36), residues: 207 loop : -0.51 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.010 0.001 PHE F 24 TYR 0.014 0.001 TYR F 223 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 621) hydrogen bonds : angle 4.17377 ( 1724) covalent geometry : bond 0.00296 (11766) covalent geometry : angle 0.54098 (16174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9398.67 seconds wall clock time: 171 minutes 47.67 seconds (10307.67 seconds total)