Starting phenix.real_space_refine on Sat Sep 12 05:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.cif Found real_map, /net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.map" model { file = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6px3_20517/09_2026/6px3_20517.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 8074 2.51 5 N 2663 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14323 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1393 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1816 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12981 SG CYS S 158 59.132 83.833 47.890 1.00358.91 S ATOM 13014 SG CYS S 163 61.737 82.243 50.744 1.00359.20 S ATOM 13051 SG CYS S 169 61.811 82.426 46.323 1.00377.57 S ATOM 12758 SG CYS S 129 58.755 80.167 51.153 1.00321.15 S ATOM 12772 SG CYS S 131 58.781 77.155 49.607 1.00322.61 S ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12910 SG CYS S 149 58.173 78.238 47.291 1.00299.48 S ATOM 13819 SG CYS S 261 37.845 88.685 19.012 1.00396.58 S ATOM 14198 SG CYS S 308 40.086 91.078 16.518 1.00413.35 S ATOM 14216 SG CYS S 310 40.442 89.010 15.411 1.00394.48 S ATOM 14250 SG CYS S 315 37.517 90.048 15.112 1.00394.57 S Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 14323 At special positions: 0 Unit cell: (93.6, 145.6, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 290 15.00 O 3260 8.00 N 2663 7.00 C 8074 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: 1.18 Conformation dependent library (CDL) restraints added in 469.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.8% alpha, 7.1% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid -50 through -37 Processing helix chain 'C' and resid -35 through -33 No H-bonds generated for 'chain 'C' and resid -35 through -33' Processing helix chain 'C' and resid -17 through -12 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.632A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.547A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.600A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.827A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid -60 through -56 removed outlier: 8.790A pdb=" N LEU C -5 " --> pdb=" O GLN C -70 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C -68 " --> pdb=" O LEU C -5 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C -3 " --> pdb=" O PHE C -68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C -66 " --> pdb=" O LEU C -3 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU C -1 " --> pdb=" O LYS C -66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB5, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.714A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 212 through 214 466 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 1.64 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: 2342 1.33 - 1.45: 5126 1.45 - 1.57: 7067 1.57 - 1.69: 578 1.69 - 1.81: 48 Bond restraints: 15161 Sorted by residual: bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.435 1.501 -0.066 1.30e-02 5.92e+03 2.54e+01 bond pdb=" C3' DG J 29 " pdb=" O3' DG J 29 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.49e+01 bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.29e+01 bond pdb=" C3' DT J 28 " pdb=" O3' DT J 28 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.16e+01 bond pdb=" C3' DC I 84 " pdb=" O3' DC I 84 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.14e+01 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 20192 2.05 - 4.09: 1426 4.09 - 6.14: 66 6.14 - 8.18: 15 8.18 - 10.23: 3 Bond angle restraints: 21702 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.41 -7.03 1.05e+00 9.07e-01 4.48e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.25 -7.25 1.10e+00 8.26e-01 4.34e+01 angle pdb=" O5' DA J 121 " pdb=" C5' DA J 121 " pdb=" C4' DA J 121 " ideal model delta sigma weight residual 109.40 113.82 -4.42 8.00e-01 1.56e+00 3.05e+01 angle pdb=" O4' DG I 102 " pdb=" C1' DG I 102 " pdb=" N9 DG I 102 " ideal model delta sigma weight residual 108.00 104.29 3.71 7.00e-01 2.04e+00 2.81e+01 ... (remaining 21697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 6839 34.59 - 69.19: 1517 69.19 - 103.78: 17 103.78 - 138.38: 0 138.38 - 172.97: 4 Dihedral angle restraints: 8377 sinusoidal: 5318 harmonic: 3059 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.03 172.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1656 0.057 - 0.113: 623 0.113 - 0.170: 137 0.170 - 0.227: 25 0.227 - 0.283: 6 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2444 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.60e-02 7.71e+00 pdb=" N9 DG J 106 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 2 1.67 - 2.48: 35 2.48 - 3.28: 14016 3.28 - 4.09: 41685 4.09 - 4.90: 65863 Warning: very small nonbonded interaction distances. Nonbonded interactions: 121601 Sorted by model distance: nonbonded pdb=" O GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 0.861 3.040 nonbonded pdb=" O GLN C -23 " pdb=" CD GLU D 102 " model vdw 1.590 3.270 nonbonded pdb=" O GLY C -25 " pdb=" OD1 ASP C 90 " model vdw 1.742 3.040 nonbonded pdb=" C GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 1.788 3.270 nonbonded pdb=" NE2 GLN C -23 " pdb=" CE1 HIS D 106 " model vdw 2.014 3.340 ... (remaining 121596 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 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'D' and resid 27 through 120) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.009 0.165 15173 Z= 0.757 Angle : 1.297 47.524 21720 Z= 0.843 Chirality : 0.062 0.283 2447 Planarity : 0.007 0.056 1760 Dihedral : 26.725 172.971 6407 Min Nonbonded Distance : 0.861 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1033 helix: 0.14 (0.19), residues: 564 sheet: -1.34 (0.57), residues: 71 loop : -1.49 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.017 0.003 TYR H 118 PHE 0.024 0.003 PHE B 61 TRP 0.005 0.002 TRP S 135 HIS 0.005 0.001 HIS C -4 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.75 (15161) covalent geometry : angle 1.04888 / 0.83 (21702) hydrogen bonds : bond 0.11466 / 7.69 ( 834) hydrogen bonds : angle 4.30700 / 3.09 ( 2077) metal coordination : bond 0.07879 / 4.74 ( 12) metal coordination : angle 26.50171 / 15.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 381 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9681 (m) cc_final: 0.9394 (p) REVERT: A 68 GLN cc_start: 0.9771 (tt0) cc_final: 0.9236 (tp-100) REVERT: A 80 THR cc_start: 0.9356 (m) cc_final: 0.8842 (p) REVERT: A 81 ASP cc_start: 0.8742 (t0) cc_final: 0.8315 (t0) REVERT: A 94 GLU cc_start: 0.8893 (tp30) cc_final: 0.8003 (tm-30) REVERT: A 105 GLU cc_start: 0.9274 (tp30) cc_final: 0.8923 (tm-30) REVERT: B 44 LYS cc_start: 0.9444 (tttt) cc_final: 0.9184 (ttpt) REVERT: B 49 LEU cc_start: 0.9752 (mt) cc_final: 0.9216 (mm) REVERT: B 59 LYS cc_start: 0.9615 (ttpt) cc_final: 0.9218 (tppp) REVERT: B 70 VAL cc_start: 0.9699 (t) cc_final: 0.9340 (p) REVERT: B 74 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8726 (pt0) REVERT: B 79 LYS cc_start: 0.9577 (mttt) cc_final: 0.8995 (tppt) REVERT: B 81 VAL cc_start: 0.9671 (t) cc_final: 0.9463 (p) REVERT: B 84 MET cc_start: 0.9403 (mmt) cc_final: 0.8442 (mmp) REVERT: B 88 TYR cc_start: 0.9481 (m-10) cc_final: 0.9239 (m-80) REVERT: B 97 LEU cc_start: 0.9271 (tp) cc_final: 0.8362 (tp) REVERT: C 25 PHE cc_start: 0.7986 (m-10) cc_final: 0.7643 (m-10) REVERT: C 39 TYR cc_start: 0.8910 (m-80) cc_final: 0.8171 (m-80) REVERT: C 56 GLU cc_start: 0.9195 (pp20) cc_final: 0.8499 (tt0) REVERT: C 68 ASN cc_start: 0.8857 (m-40) cc_final: 0.8646 (m110) REVERT: C 83 LEU cc_start: 0.9756 (mt) cc_final: 0.9489 (mt) REVERT: C 91 GLU cc_start: 0.9240 (mm-30) cc_final: 0.9005 (mp0) REVERT: C 93 LEU cc_start: 0.9648 (mt) cc_final: 0.9343 (mt) REVERT: C 110 ASN cc_start: 0.9400 (t0) cc_final: 0.9029 (m110) REVERT: C 111 ILE cc_start: 0.9305 (mt) cc_final: 0.9085 (mm) REVERT: D 34 TYR cc_start: 0.9077 (m-80) cc_final: 0.8835 (m-80) REVERT: D 40 LYS cc_start: 0.9527 (mttt) cc_final: 0.9110 (mtmm) REVERT: D 64 ASN cc_start: 0.9556 (m-40) cc_final: 0.8793 (t0) REVERT: D 96 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8885 (mtm180) REVERT: D 103 LEU cc_start: 0.9523 (mt) cc_final: 0.9247 (mt) REVERT: E 39 HIS cc_start: 0.8386 (m90) cc_final: 0.7916 (m90) REVERT: E 41 TYR cc_start: 0.8518 (m-80) cc_final: 0.8216 (m-80) REVERT: E 74 ILE cc_start: 0.9693 (mt) cc_final: 0.9346 (tt) REVERT: E 93 GLN cc_start: 0.9416 (tt0) cc_final: 0.9138 (tt0) REVERT: E 99 TYR cc_start: 0.9451 (t80) cc_final: 0.9108 (t80) REVERT: F 35 ARG cc_start: 0.9746 (ttm170) cc_final: 0.9431 (ttm110) REVERT: F 49 LEU cc_start: 0.9766 (mm) cc_final: 0.9461 (tt) REVERT: F 53 GLU cc_start: 0.9140 (tp30) cc_final: 0.8529 (tp30) REVERT: F 54 THR cc_start: 0.9664 (m) cc_final: 0.9426 (p) REVERT: F 59 LYS cc_start: 0.9783 (tttm) cc_final: 0.9460 (tppp) REVERT: F 64 ASN cc_start: 0.9660 (m-40) cc_final: 0.9011 (t0) REVERT: F 84 MET cc_start: 0.9256 (mmm) cc_final: 0.8369 (mmm) REVERT: F 85 ASP cc_start: 0.9078 (m-30) cc_final: 0.8740 (t70) REVERT: G 25 PHE cc_start: 0.9254 (m-80) cc_final: 0.8606 (m-10) REVERT: G 27 VAL cc_start: 0.8578 (m) cc_final: 0.8260 (p) REVERT: G 39 TYR cc_start: 0.9000 (m-80) cc_final: 0.8666 (m-80) REVERT: G 84 GLN cc_start: 0.9400 (tp40) cc_final: 0.9180 (tp40) REVERT: G 89 ASN cc_start: 0.9649 (m-40) cc_final: 0.9426 (m110) REVERT: G 94 ASN cc_start: 0.9700 (t0) cc_final: 0.9321 (m110) REVERT: G 95 LYS cc_start: 0.9631 (mttt) cc_final: 0.9426 (mttt) REVERT: G 101 THR cc_start: 0.9688 (m) cc_final: 0.9358 (p) REVERT: G 102 ILE cc_start: 0.9641 (mt) cc_final: 0.9309 (mt) REVERT: G 107 VAL cc_start: 0.8488 (t) cc_final: 0.8168 (m) REVERT: H 34 TYR cc_start: 0.9633 (m-80) cc_final: 0.9238 (m-10) REVERT: H 59 MET cc_start: 0.9617 (mmm) cc_final: 0.9206 (mmm) REVERT: H 68 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9231 (tm-30) REVERT: H 73 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8920 (mm-30) REVERT: H 103 LEU cc_start: 0.9700 (mt) cc_final: 0.9469 (mt) REVERT: S 103 CYS cc_start: 0.5620 (t) cc_final: 0.5355 (t) REVERT: S 203 ASN cc_start: 0.9452 (t0) cc_final: 0.9093 (m-40) REVERT: S 276 LEU cc_start: 0.9569 (tp) cc_final: 0.9250 (pt) REVERT: S 278 MET cc_start: 0.6685 (mmm) cc_final: 0.6442 (mmm) outliers start: 4 outliers final: 0 residues processed: 385 average time/residue: 0.1542 time to fit residues: 81.6313 Evaluate side-chains 239 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C -32 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS F 25 ASN F 93 GLN G 24 GLN G 38 ASN ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.042431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.029050 restraints weight = 128220.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.029967 restraints weight = 71962.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030565 restraints weight = 51173.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.030877 restraints weight = 41689.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.031100 restraints weight = 37482.994| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15173 Z= 0.253 Angle : 0.905 22.670 21720 Z= 0.455 Chirality : 0.052 0.326 2447 Planarity : 0.006 0.054 1760 Dihedral : 30.574 176.133 4337 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.23 % Allowed : 4.97 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1033 helix: 0.94 (0.20), residues: 576 sheet: -0.88 (0.63), residues: 67 loop : -1.32 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 52 TYR 0.027 0.002 TYR G 50 PHE 0.015 0.002 PHE D 67 TRP 0.005 0.002 TRP S 270 HIS 0.011 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.25 (15161) covalent geometry : angle 0.81494 / 0.45 (21702) hydrogen bonds : bond 0.07817 / 5.33 ( 834) hydrogen bonds : angle 4.05159 / 2.89 ( 2077) metal coordination : bond 0.01226 / 0.83 ( 12) metal coordination : angle 13.67486 / 9.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9608 (m) cc_final: 0.9384 (p) REVERT: A 59 GLU cc_start: 0.8890 (pm20) cc_final: 0.8412 (pm20) REVERT: A 60 LEU cc_start: 0.8307 (mm) cc_final: 0.7627 (pp) REVERT: A 68 GLN cc_start: 0.9778 (tt0) cc_final: 0.9315 (tm-30) REVERT: A 80 THR cc_start: 0.9230 (m) cc_final: 0.8920 (p) REVERT: A 90 MET cc_start: 0.9708 (tpt) cc_final: 0.9430 (tpt) REVERT: A 120 MET cc_start: 0.9397 (tpt) cc_final: 0.9187 (tpp) REVERT: B 44 LYS cc_start: 0.9511 (tttt) cc_final: 0.9254 (ttmt) REVERT: B 59 LYS cc_start: 0.9698 (ttpt) cc_final: 0.9270 (tppp) REVERT: B 68 ASP cc_start: 0.9504 (m-30) cc_final: 0.9284 (m-30) REVERT: B 84 MET cc_start: 0.9321 (mmt) cc_final: 0.8428 (mmp) REVERT: B 88 TYR cc_start: 0.9465 (m-10) cc_final: 0.9027 (m-80) REVERT: C 39 TYR cc_start: 0.8877 (m-80) cc_final: 0.8041 (m-80) REVERT: C 78 ILE cc_start: 0.9505 (mt) cc_final: 0.9241 (tp) REVERT: C 83 LEU cc_start: 0.9537 (mt) cc_final: 0.9259 (mt) REVERT: C 90 ASP cc_start: 0.8876 (t70) cc_final: 0.8097 (t70) REVERT: C 91 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9120 (mp0) REVERT: C 93 LEU cc_start: 0.9585 (mt) cc_final: 0.9273 (mt) REVERT: C 96 LEU cc_start: 0.8993 (mt) cc_final: 0.8648 (mt) REVERT: C 101 THR cc_start: 0.9451 (m) cc_final: 0.9121 (t) REVERT: C 110 ASN cc_start: 0.9514 (t0) cc_final: 0.9042 (m-40) REVERT: D 54 LYS cc_start: 0.9607 (mppt) cc_final: 0.9339 (mppt) REVERT: D 58 ILE cc_start: 0.9864 (mm) cc_final: 0.9615 (mm) REVERT: D 64 ASN cc_start: 0.9526 (m-40) cc_final: 0.9203 (t0) REVERT: D 68 GLU cc_start: 0.9268 (mp0) cc_final: 0.8751 (mm-30) REVERT: D 103 LEU cc_start: 0.9731 (mt) cc_final: 0.9313 (mt) REVERT: E 36 MET cc_start: 0.9075 (mtm) cc_final: 0.8526 (mtt) REVERT: E 39 HIS cc_start: 0.8051 (m90) cc_final: 0.7618 (m90) REVERT: E 41 TYR cc_start: 0.8636 (m-80) cc_final: 0.8334 (m-80) REVERT: E 50 GLU cc_start: 0.9626 (mp0) cc_final: 0.9376 (mp0) REVERT: E 56 LYS cc_start: 0.9391 (pttt) cc_final: 0.9136 (pptt) REVERT: E 73 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9177 (mm-30) REVERT: E 115 LYS cc_start: 0.9484 (mppt) cc_final: 0.9242 (mptt) REVERT: E 120 MET cc_start: 0.9195 (mmp) cc_final: 0.8662 (mmm) REVERT: F 31 LYS cc_start: 0.9758 (ttpt) cc_final: 0.9510 (ttpp) REVERT: F 35 ARG cc_start: 0.9782 (ttm170) cc_final: 0.9519 (ttm110) REVERT: F 49 LEU cc_start: 0.9787 (mm) cc_final: 0.8866 (tp) REVERT: F 54 THR cc_start: 0.9700 (m) cc_final: 0.9448 (p) REVERT: F 64 ASN cc_start: 0.9641 (m-40) cc_final: 0.9132 (t0) REVERT: F 68 ASP cc_start: 0.9305 (m-30) cc_final: 0.8957 (m-30) REVERT: F 85 ASP cc_start: 0.9275 (m-30) cc_final: 0.8657 (t70) REVERT: F 98 TYR cc_start: 0.8772 (m-80) cc_final: 0.8493 (m-80) REVERT: G 25 PHE cc_start: 0.9184 (m-80) cc_final: 0.8746 (m-10) REVERT: G 92 GLU cc_start: 0.9126 (mp0) cc_final: 0.8627 (mt-10) REVERT: G 94 ASN cc_start: 0.9736 (t0) cc_final: 0.9327 (m110) REVERT: G 95 LYS cc_start: 0.9649 (mttt) cc_final: 0.9443 (mttt) REVERT: G 101 THR cc_start: 0.9591 (m) cc_final: 0.9341 (p) REVERT: H 34 TYR cc_start: 0.9592 (m-80) cc_final: 0.9082 (m-10) REVERT: H 59 MET cc_start: 0.9563 (mmm) cc_final: 0.9069 (mmp) REVERT: H 68 GLU cc_start: 0.9519 (tm-30) cc_final: 0.9168 (tm-30) REVERT: H 103 LEU cc_start: 0.9675 (mt) cc_final: 0.9368 (mt) REVERT: S 103 CYS cc_start: 0.6373 (t) cc_final: 0.6114 (t) REVERT: S 113 LEU cc_start: 0.8901 (mp) cc_final: 0.8265 (mt) REVERT: S 203 ASN cc_start: 0.9536 (t0) cc_final: 0.9220 (m-40) REVERT: S 223 MET cc_start: 0.8245 (tmm) cc_final: 0.7953 (tmm) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.1421 time to fit residues: 58.9713 Evaluate side-chains 226 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 24 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.042133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028818 restraints weight = 130731.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029765 restraints weight = 73316.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030364 restraints weight = 52331.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.030739 restraints weight = 42825.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030904 restraints weight = 38211.678| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15173 Z= 0.190 Angle : 0.758 17.064 21720 Z= 0.402 Chirality : 0.048 0.348 2447 Planarity : 0.006 0.072 1760 Dihedral : 30.657 177.112 4337 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.34 % Allowed : 3.95 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1033 helix: 1.16 (0.21), residues: 572 sheet: -0.62 (0.63), residues: 66 loop : -1.12 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 52 TYR 0.039 0.002 TYR F 88 PHE 0.019 0.002 PHE E 67 TRP 0.005 0.001 TRP S 135 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (15161) covalent geometry : angle 0.70197 / 0.40 (21702) hydrogen bonds : bond 0.06054 / 4.10 ( 834) hydrogen bonds : angle 3.77513 / 2.70 ( 2077) metal coordination : bond 0.00826 / 0.48 ( 12) metal coordination : angle 9.94288 / 7.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8955 (pm20) cc_final: 0.8736 (pm20) REVERT: A 64 LYS cc_start: 0.9525 (mppt) cc_final: 0.9300 (mmtm) REVERT: A 68 GLN cc_start: 0.9789 (tt0) cc_final: 0.9334 (tm-30) REVERT: A 80 THR cc_start: 0.9225 (m) cc_final: 0.8941 (p) REVERT: A 81 ASP cc_start: 0.8454 (t70) cc_final: 0.8180 (t0) REVERT: A 90 MET cc_start: 0.9674 (tpt) cc_final: 0.9278 (tpt) REVERT: A 110 CYS cc_start: 0.9437 (t) cc_final: 0.9225 (t) REVERT: A 120 MET cc_start: 0.9397 (tpt) cc_final: 0.8914 (tpp) REVERT: B 44 LYS cc_start: 0.9536 (tttt) cc_final: 0.9240 (ttpt) REVERT: B 49 LEU cc_start: 0.9553 (mp) cc_final: 0.9322 (mm) REVERT: B 64 ASN cc_start: 0.9627 (m-40) cc_final: 0.9409 (t0) REVERT: B 68 ASP cc_start: 0.9482 (m-30) cc_final: 0.9222 (m-30) REVERT: B 74 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8888 (tm-30) REVERT: B 85 ASP cc_start: 0.8910 (m-30) cc_final: 0.8280 (t70) REVERT: B 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8441 (m-10) REVERT: C 39 TYR cc_start: 0.8917 (m-80) cc_final: 0.8306 (m-80) REVERT: C 56 GLU cc_start: 0.9223 (pp20) cc_final: 0.8902 (pp20) REVERT: C 78 ILE cc_start: 0.9600 (mt) cc_final: 0.9313 (tp) REVERT: C 83 LEU cc_start: 0.9533 (mt) cc_final: 0.9240 (mt) REVERT: C 90 ASP cc_start: 0.8845 (t70) cc_final: 0.7956 (t70) REVERT: C 91 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8976 (mp0) REVERT: C 93 LEU cc_start: 0.9551 (mt) cc_final: 0.9254 (mt) REVERT: C 96 LEU cc_start: 0.9004 (mt) cc_final: 0.8709 (mt) REVERT: C 101 THR cc_start: 0.9442 (m) cc_final: 0.9142 (t) REVERT: C 110 ASN cc_start: 0.9499 (t0) cc_final: 0.9219 (m110) REVERT: C 111 ILE cc_start: 0.9375 (mm) cc_final: 0.9083 (mm) REVERT: D 40 LYS cc_start: 0.9504 (mttt) cc_final: 0.9302 (ptpt) REVERT: D 54 LYS cc_start: 0.9612 (mppt) cc_final: 0.9311 (mppt) REVERT: D 64 ASN cc_start: 0.9511 (m-40) cc_final: 0.9165 (t0) REVERT: D 68 GLU cc_start: 0.9267 (mp0) cc_final: 0.8775 (mm-30) REVERT: D 91 ILE cc_start: 0.9753 (tp) cc_final: 0.9509 (tt) REVERT: D 103 LEU cc_start: 0.9761 (mt) cc_final: 0.9398 (mt) REVERT: E 39 HIS cc_start: 0.8031 (m90) cc_final: 0.7780 (m90) REVERT: E 41 TYR cc_start: 0.8580 (m-80) cc_final: 0.8374 (m-80) REVERT: E 73 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9167 (mm-30) REVERT: E 79 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9261 (tmtt) REVERT: E 103 LEU cc_start: 0.9704 (tt) cc_final: 0.9409 (pp) REVERT: E 105 GLU cc_start: 0.9577 (tp30) cc_final: 0.9204 (tm-30) REVERT: E 120 MET cc_start: 0.9299 (mmp) cc_final: 0.8628 (mmm) REVERT: F 31 LYS cc_start: 0.9754 (ttpt) cc_final: 0.9408 (ttpp) REVERT: F 35 ARG cc_start: 0.9746 (ttm170) cc_final: 0.9346 (ttm110) REVERT: F 44 LYS cc_start: 0.9389 (ttmt) cc_final: 0.8814 (mtmt) REVERT: F 49 LEU cc_start: 0.9620 (mm) cc_final: 0.9285 (tp) REVERT: F 54 THR cc_start: 0.9668 (m) cc_final: 0.9445 (p) REVERT: F 62 LEU cc_start: 0.9819 (mm) cc_final: 0.9609 (mt) REVERT: F 64 ASN cc_start: 0.9694 (m-40) cc_final: 0.9145 (t0) REVERT: F 68 ASP cc_start: 0.9223 (m-30) cc_final: 0.8757 (m-30) REVERT: F 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8638 (t70) REVERT: G 25 PHE cc_start: 0.9090 (m-80) cc_final: 0.8779 (m-10) REVERT: G 61 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9136 (mm-30) REVERT: G 92 GLU cc_start: 0.9116 (mp0) cc_final: 0.8585 (mt-10) REVERT: G 94 ASN cc_start: 0.9746 (t0) cc_final: 0.9336 (m110) REVERT: G 95 LYS cc_start: 0.9643 (mttt) cc_final: 0.9437 (mttt) REVERT: G 101 THR cc_start: 0.9549 (m) cc_final: 0.9270 (p) REVERT: H 34 TYR cc_start: 0.9626 (m-80) cc_final: 0.8996 (m-10) REVERT: H 68 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9081 (tm-30) REVERT: H 103 LEU cc_start: 0.9633 (mt) cc_final: 0.9333 (mt) REVERT: S 103 CYS cc_start: 0.6536 (t) cc_final: 0.6296 (t) REVERT: S 203 ASN cc_start: 0.9604 (t0) cc_final: 0.9245 (m-40) REVERT: S 223 MET cc_start: 0.8275 (tmm) cc_final: 0.8071 (tmm) outliers start: 3 outliers final: 1 residues processed: 278 average time/residue: 0.1364 time to fit residues: 54.1416 Evaluate side-chains 223 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.041499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.028285 restraints weight = 132832.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029189 restraints weight = 75330.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.029767 restraints weight = 54193.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.030118 restraints weight = 44672.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.030283 restraints weight = 39965.761| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.004 0.064 15173 Z= 0.196 Angle : 0.732 14.973 21720 Z= 0.394 Chirality : 0.047 0.343 2447 Planarity : 0.005 0.062 1760 Dihedral : 30.707 179.513 4337 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1033 helix: 1.13 (0.21), residues: 574 sheet: -0.49 (0.64), residues: 66 loop : -1.09 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.037 0.002 TYR F 88 PHE 0.024 0.002 PHE C 25 TRP 0.005 0.001 TRP S 135 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.20 (15161) covalent geometry : angle 0.68668 / 0.39 (21702) hydrogen bonds : bond 0.06617 / 4.50 ( 834) hydrogen bonds : angle 3.76520 / 2.70 ( 2077) metal coordination : bond 0.00848 / 0.52 ( 12) metal coordination : angle 8.85331 / 6.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8728 (mm) cc_final: 0.8407 (mm) REVERT: A 62 ILE cc_start: 0.9386 (pt) cc_final: 0.8733 (pt) REVERT: A 64 LYS cc_start: 0.9580 (mppt) cc_final: 0.9197 (mmtm) REVERT: A 65 LEU cc_start: 0.9731 (mm) cc_final: 0.9487 (tp) REVERT: A 68 GLN cc_start: 0.9795 (tt0) cc_final: 0.9307 (tm-30) REVERT: A 80 THR cc_start: 0.9244 (m) cc_final: 0.8946 (p) REVERT: A 81 ASP cc_start: 0.8511 (t70) cc_final: 0.8215 (t0) REVERT: A 90 MET cc_start: 0.9722 (tpt) cc_final: 0.8868 (tpp) REVERT: A 94 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8997 (mm-30) REVERT: A 120 MET cc_start: 0.9370 (tpt) cc_final: 0.9006 (tpp) REVERT: B 44 LYS cc_start: 0.9525 (tttt) cc_final: 0.9284 (ttmt) REVERT: B 52 GLU cc_start: 0.9129 (pm20) cc_final: 0.8923 (pm20) REVERT: B 59 LYS cc_start: 0.9543 (ttpp) cc_final: 0.8483 (tmmt) REVERT: B 64 ASN cc_start: 0.9527 (m-40) cc_final: 0.9161 (t0) REVERT: B 68 ASP cc_start: 0.9490 (m-30) cc_final: 0.9207 (m-30) REVERT: B 84 MET cc_start: 0.9100 (tpt) cc_final: 0.8365 (mmm) REVERT: B 85 ASP cc_start: 0.9114 (m-30) cc_final: 0.8817 (t0) REVERT: B 88 TYR cc_start: 0.9353 (m-10) cc_final: 0.8940 (m-80) REVERT: C 39 TYR cc_start: 0.8975 (m-80) cc_final: 0.8509 (m-80) REVERT: C 56 GLU cc_start: 0.9192 (pp20) cc_final: 0.8931 (pp20) REVERT: C 78 ILE cc_start: 0.9585 (mt) cc_final: 0.9312 (tp) REVERT: C 83 LEU cc_start: 0.9518 (mt) cc_final: 0.9227 (mt) REVERT: C 90 ASP cc_start: 0.8824 (t70) cc_final: 0.7953 (t70) REVERT: C 91 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8962 (mp0) REVERT: C 93 LEU cc_start: 0.9572 (mt) cc_final: 0.9252 (mt) REVERT: C 101 THR cc_start: 0.9455 (m) cc_final: 0.9109 (t) REVERT: C 110 ASN cc_start: 0.9430 (t0) cc_final: 0.9212 (m110) REVERT: C 111 ILE cc_start: 0.9446 (mm) cc_final: 0.9046 (mm) REVERT: D 40 LYS cc_start: 0.9459 (mttt) cc_final: 0.9259 (ptpt) REVERT: D 58 ILE cc_start: 0.9857 (mm) cc_final: 0.9641 (mm) REVERT: D 59 MET cc_start: 0.9545 (mmp) cc_final: 0.9339 (mmm) REVERT: D 64 ASN cc_start: 0.9513 (m-40) cc_final: 0.8903 (t0) REVERT: D 68 GLU cc_start: 0.9272 (mp0) cc_final: 0.8551 (mp0) REVERT: E 36 MET cc_start: 0.9306 (mtm) cc_final: 0.9046 (mtt) REVERT: E 39 HIS cc_start: 0.8340 (m90) cc_final: 0.7948 (m90) REVERT: E 50 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9163 (mm-30) REVERT: E 56 LYS cc_start: 0.9329 (pptt) cc_final: 0.9018 (pptt) REVERT: E 62 ILE cc_start: 0.9030 (tp) cc_final: 0.8560 (pt) REVERT: E 67 PHE cc_start: 0.9750 (t80) cc_final: 0.9498 (t80) REVERT: E 73 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9134 (mm-30) REVERT: E 79 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9218 (tmtt) REVERT: E 105 GLU cc_start: 0.9604 (tp30) cc_final: 0.9110 (tm-30) REVERT: E 120 MET cc_start: 0.9274 (mmp) cc_final: 0.8931 (mmm) REVERT: F 31 LYS cc_start: 0.9759 (ttpt) cc_final: 0.9372 (ttpp) REVERT: F 35 ARG cc_start: 0.9739 (ttm170) cc_final: 0.9327 (ttm110) REVERT: F 44 LYS cc_start: 0.9392 (ttmt) cc_final: 0.8959 (mttt) REVERT: F 49 LEU cc_start: 0.9648 (mm) cc_final: 0.9290 (tp) REVERT: F 54 THR cc_start: 0.9672 (m) cc_final: 0.9433 (p) REVERT: F 62 LEU cc_start: 0.9790 (mm) cc_final: 0.9570 (mt) REVERT: F 64 ASN cc_start: 0.9680 (m-40) cc_final: 0.9153 (t0) REVERT: F 68 ASP cc_start: 0.9199 (m-30) cc_final: 0.8712 (m-30) REVERT: F 85 ASP cc_start: 0.9257 (m-30) cc_final: 0.8948 (m-30) REVERT: G 61 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9092 (mm-30) REVERT: G 92 GLU cc_start: 0.9085 (mp0) cc_final: 0.8571 (mt-10) REVERT: G 94 ASN cc_start: 0.9750 (t0) cc_final: 0.9358 (m110) REVERT: G 95 LYS cc_start: 0.9660 (mttt) cc_final: 0.9456 (mttt) REVERT: G 101 THR cc_start: 0.9582 (m) cc_final: 0.9310 (p) REVERT: G 104 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8069 (tp-100) REVERT: H 59 MET cc_start: 0.9655 (mmm) cc_final: 0.9067 (mmp) REVERT: H 68 GLU cc_start: 0.9525 (tm-30) cc_final: 0.9095 (tm-30) REVERT: H 103 LEU cc_start: 0.9621 (mt) cc_final: 0.9324 (mt) REVERT: S 103 CYS cc_start: 0.6625 (t) cc_final: 0.6349 (t) REVERT: S 203 ASN cc_start: 0.9618 (t0) cc_final: 0.9260 (m-40) REVERT: S 223 MET cc_start: 0.8307 (tmm) cc_final: 0.8041 (tmm) outliers start: 1 outliers final: 1 residues processed: 266 average time/residue: 0.1336 time to fit residues: 50.9529 Evaluate side-chains 211 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 chunk 126 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 128 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.039465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.026611 restraints weight = 137639.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.027432 restraints weight = 79164.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027941 restraints weight = 56877.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.028275 restraints weight = 47398.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028406 restraints weight = 42294.450| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15173 Z= 0.299 Angle : 0.844 13.186 21720 Z= 0.448 Chirality : 0.049 0.354 2447 Planarity : 0.006 0.063 1760 Dihedral : 31.150 179.923 4337 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1033 helix: 0.74 (0.20), residues: 579 sheet: -0.62 (0.65), residues: 67 loop : -1.12 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 52 TYR 0.041 0.003 TYR F 88 PHE 0.024 0.002 PHE C 25 TRP 0.011 0.003 TRP S 270 HIS 0.019 0.003 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.30 (15161) covalent geometry : angle 0.79619 / 0.45 (21702) hydrogen bonds : bond 0.11307 / 7.71 ( 834) hydrogen bonds : angle 4.21282 / 3.01 ( 2077) metal coordination : bond 0.01733 / 1.11 ( 12) metal coordination : angle 9.71333 / 7.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9345 (mp0) cc_final: 0.8972 (mp0) REVERT: A 60 LEU cc_start: 0.8888 (mm) cc_final: 0.8423 (mm) REVERT: A 64 LYS cc_start: 0.9559 (mppt) cc_final: 0.9338 (mmtm) REVERT: A 65 LEU cc_start: 0.9727 (mm) cc_final: 0.9520 (tp) REVERT: A 68 GLN cc_start: 0.9799 (tt0) cc_final: 0.9310 (tm-30) REVERT: A 81 ASP cc_start: 0.8630 (t70) cc_final: 0.8371 (t0) REVERT: A 90 MET cc_start: 0.9746 (tpt) cc_final: 0.8824 (tpp) REVERT: A 94 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9089 (mm-30) REVERT: B 44 LYS cc_start: 0.9509 (tttt) cc_final: 0.9208 (ttmm) REVERT: B 64 ASN cc_start: 0.9529 (m-40) cc_final: 0.9283 (t0) REVERT: B 68 ASP cc_start: 0.9420 (m-30) cc_final: 0.9116 (m-30) REVERT: B 85 ASP cc_start: 0.9166 (m-30) cc_final: 0.8759 (t0) REVERT: C 39 TYR cc_start: 0.9096 (m-80) cc_final: 0.8566 (m-80) REVERT: C 83 LEU cc_start: 0.9580 (mt) cc_final: 0.9261 (mp) REVERT: C 90 ASP cc_start: 0.8743 (t70) cc_final: 0.8402 (t70) REVERT: C 92 GLU cc_start: 0.8747 (tt0) cc_final: 0.8532 (tt0) REVERT: C 101 THR cc_start: 0.9439 (m) cc_final: 0.9106 (t) REVERT: C 110 ASN cc_start: 0.9442 (t0) cc_final: 0.9180 (m-40) REVERT: D 40 LYS cc_start: 0.9469 (mttt) cc_final: 0.9225 (ptpt) REVERT: D 64 ASN cc_start: 0.9495 (m-40) cc_final: 0.9140 (t0) REVERT: E 36 MET cc_start: 0.9332 (mtm) cc_final: 0.8957 (mtt) REVERT: E 39 HIS cc_start: 0.8408 (m90) cc_final: 0.7906 (m90) REVERT: E 50 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9171 (mm-30) REVERT: E 56 LYS cc_start: 0.9396 (pptt) cc_final: 0.9074 (pptt) REVERT: E 67 PHE cc_start: 0.9718 (t80) cc_final: 0.9313 (t80) REVERT: E 73 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9148 (mm-30) REVERT: E 105 GLU cc_start: 0.9610 (tp30) cc_final: 0.9137 (tm-30) REVERT: E 120 MET cc_start: 0.9391 (mmp) cc_final: 0.9027 (mmm) REVERT: F 35 ARG cc_start: 0.9715 (ttm170) cc_final: 0.9406 (ttm110) REVERT: F 44 LYS cc_start: 0.9357 (ttmt) cc_final: 0.8921 (mttt) REVERT: F 62 LEU cc_start: 0.9824 (mm) cc_final: 0.9601 (mm) REVERT: F 64 ASN cc_start: 0.9654 (m-40) cc_final: 0.9429 (t0) REVERT: F 68 ASP cc_start: 0.9276 (m-30) cc_final: 0.8710 (m-30) REVERT: F 84 MET cc_start: 0.9491 (mmm) cc_final: 0.9284 (mmm) REVERT: F 85 ASP cc_start: 0.9264 (m-30) cc_final: 0.8955 (m-30) REVERT: G 61 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9031 (mm-30) REVERT: G 92 GLU cc_start: 0.9115 (mp0) cc_final: 0.8614 (mt-10) REVERT: G 94 ASN cc_start: 0.9765 (t0) cc_final: 0.9396 (m-40) REVERT: G 101 THR cc_start: 0.9523 (m) cc_final: 0.9168 (p) REVERT: G 104 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8266 (tp-100) REVERT: H 34 TYR cc_start: 0.9775 (m-80) cc_final: 0.9492 (m-10) REVERT: H 59 MET cc_start: 0.9634 (mmm) cc_final: 0.9184 (mmm) REVERT: H 68 GLU cc_start: 0.9475 (tm-30) cc_final: 0.9069 (tm-30) REVERT: H 103 LEU cc_start: 0.9640 (mt) cc_final: 0.9368 (mt) REVERT: S 103 CYS cc_start: 0.6431 (t) cc_final: 0.6126 (t) REVERT: S 203 ASN cc_start: 0.9672 (t0) cc_final: 0.9327 (m-40) REVERT: S 223 MET cc_start: 0.8360 (tmm) cc_final: 0.8071 (tmm) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1299 time to fit residues: 46.7494 Evaluate side-chains 186 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.039901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026890 restraints weight = 136113.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027759 restraints weight = 78704.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.028295 restraints weight = 57322.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028611 restraints weight = 47686.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028776 restraints weight = 42869.032| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 15173 Z= 0.233 Angle : 0.768 16.875 21720 Z= 0.409 Chirality : 0.047 0.358 2447 Planarity : 0.006 0.082 1760 Dihedral : 31.275 178.502 4337 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1033 helix: 0.83 (0.20), residues: 581 sheet: -0.68 (0.66), residues: 67 loop : -0.99 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 52 TYR 0.043 0.002 TYR F 88 PHE 0.013 0.002 PHE E 67 TRP 0.006 0.002 TRP S 135 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (15161) covalent geometry : angle 0.71051 / 0.41 (21702) hydrogen bonds : bond 0.07849 / 5.34 ( 834) hydrogen bonds : angle 4.12011 / 2.97 ( 2077) metal coordination : bond 0.01282 / 0.80 ( 12) metal coordination : angle 10.13185 / 7.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8834 (mm) cc_final: 0.7776 (tp) REVERT: A 64 LYS cc_start: 0.9590 (mppt) cc_final: 0.9323 (mppt) REVERT: A 68 GLN cc_start: 0.9783 (tt0) cc_final: 0.9286 (tm-30) REVERT: A 73 GLU cc_start: 0.9245 (mp0) cc_final: 0.9010 (mp0) REVERT: A 81 ASP cc_start: 0.8576 (t70) cc_final: 0.8356 (t0) REVERT: A 90 MET cc_start: 0.9725 (tpt) cc_final: 0.8837 (tpp) REVERT: A 94 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8954 (mm-30) REVERT: A 120 MET cc_start: 0.9505 (tpp) cc_final: 0.9141 (tpp) REVERT: B 44 LYS cc_start: 0.9493 (tttt) cc_final: 0.9179 (ttmm) REVERT: B 59 LYS cc_start: 0.9288 (tmmt) cc_final: 0.9054 (tmmt) REVERT: B 63 GLU cc_start: 0.9536 (pm20) cc_final: 0.9309 (pm20) REVERT: B 64 ASN cc_start: 0.9645 (m-40) cc_final: 0.9277 (t0) REVERT: B 68 ASP cc_start: 0.9370 (m-30) cc_final: 0.9096 (m-30) REVERT: B 84 MET cc_start: 0.9172 (tpp) cc_final: 0.8958 (mmm) REVERT: B 85 ASP cc_start: 0.9183 (m-30) cc_final: 0.8688 (t0) REVERT: B 88 TYR cc_start: 0.9433 (m-80) cc_final: 0.9198 (m-80) REVERT: C 39 TYR cc_start: 0.9035 (m-80) cc_final: 0.8602 (m-80) REVERT: C 56 GLU cc_start: 0.9219 (pp20) cc_final: 0.8948 (pp20) REVERT: C 83 LEU cc_start: 0.9556 (mt) cc_final: 0.9261 (mt) REVERT: C 90 ASP cc_start: 0.8748 (t70) cc_final: 0.8416 (t0) REVERT: C 101 THR cc_start: 0.9437 (m) cc_final: 0.9090 (t) REVERT: C 110 ASN cc_start: 0.9470 (t0) cc_final: 0.9194 (m-40) REVERT: C 111 ILE cc_start: 0.9529 (mm) cc_final: 0.9178 (mm) REVERT: D 58 ILE cc_start: 0.9877 (mm) cc_final: 0.9647 (mm) REVERT: D 64 ASN cc_start: 0.9444 (m-40) cc_final: 0.9033 (t0) REVERT: D 68 GLU cc_start: 0.9259 (mp0) cc_final: 0.8531 (mp0) REVERT: E 36 MET cc_start: 0.9292 (mtm) cc_final: 0.8969 (mtt) REVERT: E 39 HIS cc_start: 0.8386 (m90) cc_final: 0.7885 (m90) REVERT: E 50 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9182 (mm-30) REVERT: E 56 LYS cc_start: 0.9415 (pptt) cc_final: 0.9100 (pptt) REVERT: E 67 PHE cc_start: 0.9673 (t80) cc_final: 0.9298 (t80) REVERT: E 73 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9092 (mm-30) REVERT: E 79 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9285 (tttm) REVERT: E 85 GLN cc_start: 0.9364 (mt0) cc_final: 0.9156 (mt0) REVERT: E 105 GLU cc_start: 0.9566 (tp30) cc_final: 0.9070 (tm-30) REVERT: E 120 MET cc_start: 0.9404 (mmp) cc_final: 0.8826 (mmm) REVERT: F 35 ARG cc_start: 0.9751 (ttm170) cc_final: 0.9469 (ttm110) REVERT: F 44 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8931 (mttt) REVERT: F 68 ASP cc_start: 0.9059 (m-30) cc_final: 0.8431 (m-30) REVERT: F 85 ASP cc_start: 0.9251 (m-30) cc_final: 0.8957 (m-30) REVERT: G 61 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9029 (mm-30) REVERT: G 92 GLU cc_start: 0.9042 (mp0) cc_final: 0.8665 (mt-10) REVERT: G 94 ASN cc_start: 0.9749 (t0) cc_final: 0.9359 (m-40) REVERT: G 95 LYS cc_start: 0.9447 (mtmm) cc_final: 0.9188 (mttt) REVERT: G 101 THR cc_start: 0.9532 (m) cc_final: 0.9160 (p) REVERT: H 34 TYR cc_start: 0.9753 (m-80) cc_final: 0.9489 (m-10) REVERT: H 59 MET cc_start: 0.9679 (mmm) cc_final: 0.9169 (mmp) REVERT: H 103 LEU cc_start: 0.9609 (mt) cc_final: 0.9354 (mt) REVERT: S 103 CYS cc_start: 0.6263 (t) cc_final: 0.5967 (t) REVERT: S 203 ASN cc_start: 0.9678 (t0) cc_final: 0.9339 (m-40) REVERT: S 223 MET cc_start: 0.8348 (tmm) cc_final: 0.8043 (tmm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1308 time to fit residues: 45.9477 Evaluate side-chains 191 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 40.0000 chunk 90 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 40.0000 chunk 79 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.039191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.026415 restraints weight = 141153.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.027208 restraints weight = 81534.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.027727 restraints weight = 59603.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.027983 restraints weight = 49757.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028096 restraints weight = 45188.364| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 15173 Z= 0.247 Angle : 0.776 16.075 21720 Z= 0.419 Chirality : 0.047 0.353 2447 Planarity : 0.006 0.074 1760 Dihedral : 31.349 179.742 4337 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.23 % Allowed : 2.15 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1033 helix: 0.79 (0.21), residues: 577 sheet: -0.83 (0.65), residues: 67 loop : -0.91 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 96 TYR 0.031 0.002 TYR F 88 PHE 0.031 0.002 PHE A 104 TRP 0.007 0.002 TRP S 135 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.25 (15161) covalent geometry : angle 0.73080 / 0.42 (21702) hydrogen bonds : bond 0.08826 / 6.01 ( 834) hydrogen bonds : angle 4.18427 / 3.00 ( 2077) metal coordination : bond 0.02236 / 1.28 ( 12) metal coordination : angle 9.06189 / 6.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9423 (mp0) cc_final: 0.9043 (mp0) REVERT: A 51 ILE cc_start: 0.9591 (mm) cc_final: 0.9353 (mm) REVERT: A 64 LYS cc_start: 0.9625 (mppt) cc_final: 0.9298 (mmtm) REVERT: A 68 GLN cc_start: 0.9790 (tt0) cc_final: 0.9284 (tm-30) REVERT: A 90 MET cc_start: 0.9681 (tpt) cc_final: 0.8662 (tpp) REVERT: A 94 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8904 (mm-30) REVERT: A 99 TYR cc_start: 0.9545 (t80) cc_final: 0.9169 (t80) REVERT: A 120 MET cc_start: 0.9578 (tpp) cc_final: 0.9295 (tpp) REVERT: B 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.9119 (ttpt) REVERT: B 64 ASN cc_start: 0.9615 (m-40) cc_final: 0.9224 (t0) REVERT: B 68 ASP cc_start: 0.9376 (m-30) cc_final: 0.9001 (m-30) REVERT: B 84 MET cc_start: 0.9197 (tpp) cc_final: 0.8971 (mmm) REVERT: B 88 TYR cc_start: 0.9463 (m-80) cc_final: 0.9093 (m-80) REVERT: C 39 TYR cc_start: 0.9018 (m-80) cc_final: 0.8603 (m-80) REVERT: C 56 GLU cc_start: 0.8999 (pp20) cc_final: 0.8716 (pp20) REVERT: C 83 LEU cc_start: 0.9564 (mt) cc_final: 0.9362 (mp) REVERT: C 90 ASP cc_start: 0.8773 (t70) cc_final: 0.8392 (t0) REVERT: C 91 GLU cc_start: 0.9010 (mp0) cc_final: 0.8799 (mp0) REVERT: C 101 THR cc_start: 0.9437 (m) cc_final: 0.9127 (t) REVERT: C 110 ASN cc_start: 0.9476 (t0) cc_final: 0.9154 (m110) REVERT: D 58 ILE cc_start: 0.9872 (mm) cc_final: 0.9647 (mm) REVERT: D 59 MET cc_start: 0.9548 (mmp) cc_final: 0.9323 (mmm) REVERT: D 64 ASN cc_start: 0.9435 (m-40) cc_final: 0.8755 (t0) REVERT: D 68 GLU cc_start: 0.9176 (mp0) cc_final: 0.8428 (mp0) REVERT: E 36 MET cc_start: 0.9310 (mtm) cc_final: 0.8991 (mtt) REVERT: E 39 HIS cc_start: 0.8338 (m90) cc_final: 0.7855 (m90) REVERT: E 50 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9182 (mm-30) REVERT: E 56 LYS cc_start: 0.9441 (pptt) cc_final: 0.9122 (pptt) REVERT: E 67 PHE cc_start: 0.9629 (t80) cc_final: 0.9207 (t80) REVERT: E 73 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9093 (mm-30) REVERT: E 79 LYS cc_start: 0.9661 (mmmm) cc_final: 0.9398 (tppt) REVERT: E 85 GLN cc_start: 0.9322 (mt0) cc_final: 0.9097 (mt0) REVERT: E 105 GLU cc_start: 0.9547 (tp30) cc_final: 0.9077 (tm-30) REVERT: E 120 MET cc_start: 0.9348 (mmp) cc_final: 0.8810 (mmm) REVERT: F 64 ASN cc_start: 0.9447 (t0) cc_final: 0.9153 (t0) REVERT: F 68 ASP cc_start: 0.8906 (m-30) cc_final: 0.8518 (m-30) REVERT: F 85 ASP cc_start: 0.9185 (m-30) cc_final: 0.8910 (m-30) REVERT: G 92 GLU cc_start: 0.9102 (mp0) cc_final: 0.8745 (mt-10) REVERT: G 94 ASN cc_start: 0.9756 (t0) cc_final: 0.9361 (m-40) REVERT: G 95 LYS cc_start: 0.9478 (mtmm) cc_final: 0.9251 (mttt) REVERT: G 101 THR cc_start: 0.9531 (m) cc_final: 0.9150 (p) REVERT: H 34 TYR cc_start: 0.9751 (m-80) cc_final: 0.9526 (m-10) REVERT: H 59 MET cc_start: 0.9674 (mmm) cc_final: 0.9190 (mmp) REVERT: H 76 ARG cc_start: 0.8940 (ptp90) cc_final: 0.8589 (ptp90) REVERT: H 103 LEU cc_start: 0.9661 (mt) cc_final: 0.9370 (mt) REVERT: S 103 CYS cc_start: 0.6527 (t) cc_final: 0.6235 (t) REVERT: S 203 ASN cc_start: 0.9697 (t0) cc_final: 0.9368 (m-40) REVERT: S 223 MET cc_start: 0.8335 (tmm) cc_final: 0.8017 (tmm) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.1338 time to fit residues: 45.3254 Evaluate side-chains 189 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.040544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027927 restraints weight = 133980.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028817 restraints weight = 75320.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.029396 restraints weight = 54187.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029739 restraints weight = 44499.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.029832 restraints weight = 39731.220| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 15173 Z= 0.162 Angle : 0.726 15.894 21720 Z= 0.396 Chirality : 0.047 0.350 2447 Planarity : 0.005 0.065 1760 Dihedral : 31.264 178.712 4337 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1033 helix: 0.88 (0.21), residues: 578 sheet: -0.74 (0.65), residues: 66 loop : -0.82 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 52 TYR 0.040 0.002 TYR F 88 PHE 0.024 0.002 PHE A 104 TRP 0.005 0.002 TRP S 135 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (15161) covalent geometry : angle 0.68336 / 0.39 (21702) hydrogen bonds : bond 0.05629 / 3.84 ( 834) hydrogen bonds : angle 3.94952 / 2.83 ( 2077) metal coordination : bond 0.00859 / 0.52 ( 12) metal coordination : angle 8.54938 / 6.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9308 (mp0) cc_final: 0.8904 (mp0) REVERT: A 51 ILE cc_start: 0.9531 (mm) cc_final: 0.9230 (mm) REVERT: A 59 GLU cc_start: 0.8754 (pm20) cc_final: 0.8552 (pm20) REVERT: A 64 LYS cc_start: 0.9634 (mppt) cc_final: 0.9358 (mppt) REVERT: A 68 GLN cc_start: 0.9801 (tt0) cc_final: 0.9268 (tm-30) REVERT: A 87 SER cc_start: 0.9652 (m) cc_final: 0.9330 (p) REVERT: A 90 MET cc_start: 0.9697 (tpt) cc_final: 0.8791 (tpp) REVERT: A 94 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8993 (mm-30) REVERT: A 99 TYR cc_start: 0.9539 (t80) cc_final: 0.9265 (t80) REVERT: A 110 CYS cc_start: 0.9605 (t) cc_final: 0.9401 (t) REVERT: A 120 MET cc_start: 0.9486 (tpp) cc_final: 0.9242 (tpp) REVERT: B 44 LYS cc_start: 0.9462 (tttt) cc_final: 0.9138 (ttmm) REVERT: B 59 LYS cc_start: 0.9345 (pptt) cc_final: 0.9054 (pptt) REVERT: B 63 GLU cc_start: 0.9660 (pm20) cc_final: 0.9426 (pm20) REVERT: B 64 ASN cc_start: 0.9616 (m-40) cc_final: 0.9233 (t0) REVERT: B 68 ASP cc_start: 0.9354 (m-30) cc_final: 0.9091 (m-30) REVERT: B 85 ASP cc_start: 0.9117 (m-30) cc_final: 0.8689 (t0) REVERT: C 39 TYR cc_start: 0.8982 (m-80) cc_final: 0.8579 (m-80) REVERT: C 56 GLU cc_start: 0.9118 (pp20) cc_final: 0.8844 (pp20) REVERT: C 62 ILE cc_start: 0.9693 (pt) cc_final: 0.9475 (pt) REVERT: C 83 LEU cc_start: 0.9560 (mt) cc_final: 0.9280 (mt) REVERT: C 90 ASP cc_start: 0.8753 (t70) cc_final: 0.8364 (t0) REVERT: C 91 GLU cc_start: 0.9005 (mp0) cc_final: 0.8785 (mp0) REVERT: C 110 ASN cc_start: 0.9484 (t0) cc_final: 0.9111 (m110) REVERT: D 58 ILE cc_start: 0.9858 (mm) cc_final: 0.9632 (mm) REVERT: D 59 MET cc_start: 0.9537 (mmp) cc_final: 0.9277 (mmm) REVERT: D 64 ASN cc_start: 0.9441 (m-40) cc_final: 0.9042 (t0) REVERT: D 68 GLU cc_start: 0.9322 (mp0) cc_final: 0.8796 (pm20) REVERT: E 36 MET cc_start: 0.9327 (mtm) cc_final: 0.8961 (mtt) REVERT: E 39 HIS cc_start: 0.8299 (m90) cc_final: 0.7813 (m90) REVERT: E 50 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9159 (mm-30) REVERT: E 56 LYS cc_start: 0.9426 (pptt) cc_final: 0.9101 (pptt) REVERT: E 67 PHE cc_start: 0.9604 (t80) cc_final: 0.9241 (t80) REVERT: E 79 LYS cc_start: 0.9674 (mmmm) cc_final: 0.9310 (tmtt) REVERT: E 85 GLN cc_start: 0.9349 (mt0) cc_final: 0.9081 (mt0) REVERT: E 86 SER cc_start: 0.9539 (p) cc_final: 0.9149 (p) REVERT: E 90 MET cc_start: 0.9523 (mmp) cc_final: 0.9069 (mmp) REVERT: E 120 MET cc_start: 0.9427 (mmp) cc_final: 0.8866 (mmm) REVERT: F 84 MET cc_start: 0.9616 (mmm) cc_final: 0.9328 (mmm) REVERT: F 85 ASP cc_start: 0.9196 (m-30) cc_final: 0.8976 (m-30) REVERT: G 61 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9069 (mm-30) REVERT: G 94 ASN cc_start: 0.9732 (t0) cc_final: 0.9360 (m-40) REVERT: G 101 THR cc_start: 0.9538 (m) cc_final: 0.9297 (p) REVERT: H 34 TYR cc_start: 0.9638 (m-80) cc_final: 0.9140 (m-10) REVERT: H 59 MET cc_start: 0.9651 (mmm) cc_final: 0.9185 (mmp) REVERT: H 103 LEU cc_start: 0.9575 (mt) cc_final: 0.9353 (mt) REVERT: S 103 CYS cc_start: 0.6346 (t) cc_final: 0.6064 (t) REVERT: S 203 ASN cc_start: 0.9687 (t0) cc_final: 0.9357 (m-40) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1234 time to fit residues: 43.3370 Evaluate side-chains 193 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 107 optimal weight: 0.5980 chunk 91 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 89 optimal weight: 40.0000 chunk 108 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 ASN S 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.040628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027728 restraints weight = 132724.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.028617 restraints weight = 74093.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.029202 restraints weight = 53295.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029502 restraints weight = 43887.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.029730 restraints weight = 39659.416| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15173 Z= 0.159 Angle : 0.732 14.356 21720 Z= 0.399 Chirality : 0.046 0.358 2447 Planarity : 0.006 0.080 1760 Dihedral : 31.082 177.810 4337 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.23 % Allowed : 0.56 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1033 helix: 0.81 (0.21), residues: 578 sheet: -0.64 (0.65), residues: 66 loop : -0.80 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.043 0.002 TYR F 98 PHE 0.023 0.002 PHE A 104 TRP 0.004 0.001 TRP S 270 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (15161) covalent geometry : angle 0.69728 / 0.40 (21702) hydrogen bonds : bond 0.05227 / 3.57 ( 834) hydrogen bonds : angle 3.97488 / 2.90 ( 2077) metal coordination : bond 0.00742 / 0.44 ( 12) metal coordination : angle 7.77627 / 5.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9535 (mppt) cc_final: 0.9312 (mptt) REVERT: A 68 GLN cc_start: 0.9781 (tt0) cc_final: 0.9246 (tm-30) REVERT: A 87 SER cc_start: 0.9619 (m) cc_final: 0.9281 (p) REVERT: A 90 MET cc_start: 0.9736 (tpt) cc_final: 0.8852 (tpp) REVERT: A 94 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8920 (mm-30) REVERT: A 99 TYR cc_start: 0.9506 (t80) cc_final: 0.9267 (t80) REVERT: A 120 MET cc_start: 0.9550 (tpp) cc_final: 0.9247 (tpp) REVERT: B 44 LYS cc_start: 0.9443 (tttt) cc_final: 0.9121 (ttmm) REVERT: B 59 LYS cc_start: 0.9329 (pptt) cc_final: 0.9064 (pptt) REVERT: B 63 GLU cc_start: 0.9618 (pm20) cc_final: 0.9364 (pm20) REVERT: B 64 ASN cc_start: 0.9630 (m-40) cc_final: 0.9258 (t0) REVERT: B 68 ASP cc_start: 0.9366 (m-30) cc_final: 0.9129 (m-30) REVERT: B 84 MET cc_start: 0.9160 (tpt) cc_final: 0.8881 (tpp) REVERT: B 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8945 (t0) REVERT: B 88 TYR cc_start: 0.9408 (m-80) cc_final: 0.7952 (m-10) REVERT: C 39 TYR cc_start: 0.8974 (m-80) cc_final: 0.8530 (m-80) REVERT: C 56 GLU cc_start: 0.9107 (pp20) cc_final: 0.8849 (pp20) REVERT: C 83 LEU cc_start: 0.9553 (mt) cc_final: 0.9290 (mt) REVERT: C 90 ASP cc_start: 0.8799 (t70) cc_final: 0.8401 (t0) REVERT: C 91 GLU cc_start: 0.9005 (mp0) cc_final: 0.8788 (mp0) REVERT: C 110 ASN cc_start: 0.9479 (t0) cc_final: 0.9098 (m110) REVERT: D 40 LYS cc_start: 0.9412 (mttt) cc_final: 0.9024 (mtmm) REVERT: D 54 LYS cc_start: 0.9746 (mmmm) cc_final: 0.9504 (mmmm) REVERT: D 58 ILE cc_start: 0.9853 (mm) cc_final: 0.9637 (mm) REVERT: D 59 MET cc_start: 0.9598 (mmp) cc_final: 0.9271 (mmm) REVERT: E 36 MET cc_start: 0.9315 (mtm) cc_final: 0.8978 (mtt) REVERT: E 39 HIS cc_start: 0.8310 (m90) cc_final: 0.7803 (m90) REVERT: E 50 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9146 (mm-30) REVERT: E 56 LYS cc_start: 0.9418 (pptt) cc_final: 0.9089 (pptt) REVERT: E 67 PHE cc_start: 0.9548 (t80) cc_final: 0.9177 (t80) REVERT: E 79 LYS cc_start: 0.9660 (mmmm) cc_final: 0.9320 (tmtt) REVERT: E 85 GLN cc_start: 0.9362 (mt0) cc_final: 0.9102 (mt0) REVERT: E 86 SER cc_start: 0.9559 (p) cc_final: 0.9195 (p) REVERT: E 90 MET cc_start: 0.9470 (mmp) cc_final: 0.9093 (mmp) REVERT: E 120 MET cc_start: 0.9433 (mmp) cc_final: 0.8871 (mmm) REVERT: F 64 ASN cc_start: 0.9595 (t0) cc_final: 0.9223 (t0) REVERT: F 84 MET cc_start: 0.9599 (mmm) cc_final: 0.9258 (mmm) REVERT: F 88 TYR cc_start: 0.9260 (m-80) cc_final: 0.9000 (m-80) REVERT: G 61 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9104 (mm-30) REVERT: G 94 ASN cc_start: 0.9646 (t0) cc_final: 0.9191 (m-40) REVERT: G 101 THR cc_start: 0.9568 (m) cc_final: 0.9297 (p) REVERT: H 59 MET cc_start: 0.9649 (mmm) cc_final: 0.9187 (mmp) REVERT: S 103 CYS cc_start: 0.6218 (t) cc_final: 0.5945 (t) REVERT: S 203 ASN cc_start: 0.9675 (t0) cc_final: 0.9332 (m-40) REVERT: S 306 GLN cc_start: 0.5425 (OUTLIER) cc_final: 0.4870 (pp30) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.1232 time to fit residues: 43.7279 Evaluate side-chains 198 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 54 optimal weight: 0.0970 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.039914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027133 restraints weight = 133357.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027983 restraints weight = 75931.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028539 restraints weight = 54955.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.028822 restraints weight = 45138.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.029104 restraints weight = 40876.510| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15173 Z= 0.181 Angle : 0.728 13.617 21720 Z= 0.397 Chirality : 0.046 0.362 2447 Planarity : 0.006 0.063 1760 Dihedral : 31.073 177.822 4337 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.26), residues: 1033 helix: 0.67 (0.21), residues: 579 sheet: -0.48 (0.66), residues: 66 loop : -0.81 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 35 TYR 0.042 0.002 TYR F 98 PHE 0.018 0.001 PHE A 104 TRP 0.005 0.002 TRP S 270 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (15161) covalent geometry : angle 0.69222 / 0.40 (21702) hydrogen bonds : bond 0.06579 / 4.48 ( 834) hydrogen bonds : angle 4.02741 / 2.95 ( 2077) metal coordination : bond 0.00912 / 0.56 ( 12) metal coordination : angle 7.90158 / 5.66 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9026 (mm-30) REVERT: A 64 LYS cc_start: 0.9552 (mppt) cc_final: 0.9297 (mmtm) REVERT: A 68 GLN cc_start: 0.9747 (tt0) cc_final: 0.9174 (tm-30) REVERT: A 87 SER cc_start: 0.9637 (m) cc_final: 0.9303 (p) REVERT: A 90 MET cc_start: 0.9742 (tpt) cc_final: 0.8859 (tpp) REVERT: A 94 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9012 (mm-30) REVERT: A 99 TYR cc_start: 0.9508 (t80) cc_final: 0.9282 (t80) REVERT: A 105 GLU cc_start: 0.9108 (pp20) cc_final: 0.8848 (pp20) REVERT: A 106 ASP cc_start: 0.9248 (m-30) cc_final: 0.8699 (m-30) REVERT: A 120 MET cc_start: 0.9496 (tpp) cc_final: 0.9236 (tpp) REVERT: B 44 LYS cc_start: 0.9440 (tttt) cc_final: 0.9060 (ttmm) REVERT: B 59 LYS cc_start: 0.9363 (pptt) cc_final: 0.9061 (pptt) REVERT: B 63 GLU cc_start: 0.9604 (pm20) cc_final: 0.9353 (pm20) REVERT: B 64 ASN cc_start: 0.9629 (m-40) cc_final: 0.9273 (t0) REVERT: B 68 ASP cc_start: 0.9381 (m-30) cc_final: 0.9135 (m-30) REVERT: B 85 ASP cc_start: 0.9255 (m-30) cc_final: 0.8836 (t0) REVERT: C 39 TYR cc_start: 0.8984 (m-80) cc_final: 0.8628 (m-80) REVERT: C 62 ILE cc_start: 0.9636 (pt) cc_final: 0.9431 (pt) REVERT: C 83 LEU cc_start: 0.9563 (mt) cc_final: 0.9355 (mp) REVERT: C 90 ASP cc_start: 0.8812 (t70) cc_final: 0.8420 (t0) REVERT: C 91 GLU cc_start: 0.9032 (mp0) cc_final: 0.8826 (mp0) REVERT: C 110 ASN cc_start: 0.9506 (t0) cc_final: 0.9083 (m110) REVERT: D 40 LYS cc_start: 0.9401 (mttt) cc_final: 0.8986 (mtmm) REVERT: D 58 ILE cc_start: 0.9860 (mm) cc_final: 0.9610 (mm) REVERT: D 59 MET cc_start: 0.9591 (mmp) cc_final: 0.9245 (mmm) REVERT: D 65 ASP cc_start: 0.9472 (t0) cc_final: 0.9032 (t70) REVERT: E 36 MET cc_start: 0.9360 (mtm) cc_final: 0.9016 (mtt) REVERT: E 39 HIS cc_start: 0.8313 (m90) cc_final: 0.7807 (m90) REVERT: E 50 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9166 (mm-30) REVERT: E 56 LYS cc_start: 0.9433 (pptt) cc_final: 0.9101 (pptt) REVERT: E 67 PHE cc_start: 0.9552 (t80) cc_final: 0.9152 (t80) REVERT: E 85 GLN cc_start: 0.9372 (mt0) cc_final: 0.9117 (mt0) REVERT: E 86 SER cc_start: 0.9540 (p) cc_final: 0.9158 (p) REVERT: E 90 MET cc_start: 0.9483 (mmp) cc_final: 0.9222 (mmp) REVERT: E 120 MET cc_start: 0.9412 (mmp) cc_final: 0.8856 (mmm) REVERT: F 64 ASN cc_start: 0.9512 (t0) cc_final: 0.9152 (t0) REVERT: F 84 MET cc_start: 0.9582 (mmm) cc_final: 0.9256 (mmm) REVERT: F 88 TYR cc_start: 0.9276 (m-80) cc_final: 0.9031 (m-80) REVERT: G 92 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8904 (tt0) REVERT: G 94 ASN cc_start: 0.9651 (t0) cc_final: 0.9216 (m-40) REVERT: G 101 THR cc_start: 0.9564 (m) cc_final: 0.9253 (p) REVERT: H 59 MET cc_start: 0.9640 (mmm) cc_final: 0.9182 (mmp) REVERT: H 99 LEU cc_start: 0.9222 (mm) cc_final: 0.8990 (mt) REVERT: H 103 LEU cc_start: 0.9597 (mt) cc_final: 0.9215 (mt) REVERT: S 103 CYS cc_start: 0.6272 (t) cc_final: 0.6014 (t) REVERT: S 203 ASN cc_start: 0.9673 (t0) cc_final: 0.9355 (m-40) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1258 time to fit residues: 43.1467 Evaluate side-chains 191 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 88 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 121 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 84 optimal weight: 40.0000 overall best weight: 7.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.038331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.025891 restraints weight = 143952.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.026687 restraints weight = 83790.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027213 restraints weight = 61245.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.027518 restraints weight = 50932.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027707 restraints weight = 45751.147| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 15173 Z= 0.276 Angle : 0.811 14.772 21720 Z= 0.440 Chirality : 0.048 0.357 2447 Planarity : 0.006 0.076 1760 Dihedral : 31.401 178.239 4337 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.26), residues: 1033 helix: 0.36 (0.20), residues: 579 sheet: -0.82 (0.63), residues: 72 loop : -0.87 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 96 TYR 0.039 0.003 TYR F 98 PHE 0.023 0.002 PHE C 25 TRP 0.010 0.002 TRP S 270 HIS 0.010 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.28 (15161) covalent geometry : angle 0.77002 / 0.44 (21702) hydrogen bonds : bond 0.10201 / 6.93 ( 834) hydrogen bonds : angle 4.39141 / 3.22 ( 2077) metal coordination : bond 0.01683 / 1.03 ( 12) metal coordination : angle 8.91190 / 6.21 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.54 seconds wall clock time: 58 minutes 3.69 seconds (3483.69 seconds total)