Starting phenix.real_space_refine on Sun Sep 13 00:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5y_22684/09_2026/7k5y_22684.cif" } resolution = 2.76 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= -0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 394 5.49 5 S 32 5.16 5 C 10240 2.51 5 N 3340 2.21 5 O 4252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 18258 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 3.45, per 1000 atoms: 0.19 Number of scatterers: 18258 At special positions: 0 Unit cell: (133.056, 121.968, 197.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 394 15.00 O 4252 8.00 N 3340 7.00 C 10240 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: 1.52 Conformation dependent library (CDL) restraints added in 489.5 milliseconds 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 49.0% alpha, 20.8% beta 194 base pairs and 357 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.801A 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 removed outlier: 3.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.353A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 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 76 removed outlier: 3.604A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.321A 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 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.516A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.600A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.737A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 removed outlier: 3.639A pdb=" N LYS U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 71 through 74' Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.726A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.112A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.587A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.601A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.999A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.753A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.778A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.808A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.602A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.859A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 56 through 57 612 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 504 hydrogen bonds 1008 hydrogen bond angles 0 basepair planarities 194 basepair parallelities 357 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 2.04 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: 3473 1.33 - 1.45: 6143 1.45 - 1.57: 8954 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19408 Sorted by residual: bond pdb=" N SER M 26 " pdb=" CA SER M 26 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.50e+01 bond pdb=" C3' DT I 34 " pdb=" C2' DT I 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC I 35 " pdb=" C2' DC I 35 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I 120 " pdb=" C2' DC I 120 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.44e+00 bond pdb=" C3' DC J 88 " pdb=" C2' DC J 88 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 ... (remaining 19403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 25192 1.32 - 2.65: 2436 2.65 - 3.97: 251 3.97 - 5.29: 27 5.29 - 6.62: 9 Bond angle restraints: 27915 Sorted by residual: angle pdb=" O4' DT I 176 " pdb=" C1' DT I 176 " pdb=" N1 DT I 176 " ideal model delta sigma weight residual 108.00 111.51 -3.51 7.00e-01 2.04e+00 2.51e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.75 -2.85 6.00e-01 2.78e+00 2.26e+01 angle pdb=" N3 DT J 42 " pdb=" C4 DT J 42 " pdb=" O4 DT J 42 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DG J 128 " pdb=" C1' DG J 128 " pdb=" N9 DG J 128 " ideal model delta sigma weight residual 108.00 111.24 -3.24 7.00e-01 2.04e+00 2.15e+01 angle pdb=" N3 DT J 166 " pdb=" C4 DT J 166 " pdb=" O4 DT J 166 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 27910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 8535 34.24 - 68.47: 2039 68.47 - 102.71: 22 102.71 - 136.95: 3 136.95 - 171.18: 2 Dihedral angle restraints: 10601 sinusoidal: 6846 harmonic: 3755 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 48.82 171.18 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 51.89 168.11 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1998 0.038 - 0.076: 831 0.076 - 0.113: 270 0.113 - 0.151: 46 0.151 - 0.189: 7 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU M 252 " pdb=" CB LEU M 252 " pdb=" CD1 LEU M 252 " pdb=" CD2 LEU M 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" C3' DT J 153 " pdb=" C4' DT J 153 " pdb=" O3' DT J 153 " pdb=" C2' DT J 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" C3' DC J 133 " pdb=" C4' DC J 133 " pdb=" O3' DC J 133 " pdb=" C2' DC J 133 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3149 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO M 158 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 103 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " 0.021 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 45 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " -0.002 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 491 2.67 - 3.22: 15344 3.22 - 3.78: 33372 3.78 - 4.34: 45180 4.34 - 4.90: 64961 Nonbonded interactions: 159348 Sorted by model distance: nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 251 " model vdw 2.108 3.120 nonbonded pdb=" O SER N 156 " pdb=" OG1 THR N 263 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP U 71 " pdb=" NZ LYS U 74 " model vdw 2.224 3.120 nonbonded pdb=" OG SER H 56 " pdb=" OP2 DA I 45 " model vdw 2.258 3.040 nonbonded pdb=" O GLN N 155 " pdb=" NE2 GLN N 261 " model vdw 2.275 3.120 ... (remaining 159343 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.006 0.048 19408 Z= 0.522 Angle : 0.792 6.616 27915 Z= 0.678 Chirality : 0.045 0.189 3152 Planarity : 0.004 0.058 2154 Dihedral : 27.043 171.183 8195 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.74 (0.23), residues: 1271 helix: 2.37 (0.21), residues: 584 sheet: 0.64 (0.33), residues: 252 loop : -0.19 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 69 TYR 0.026 0.002 TYR N 201 PHE 0.015 0.002 PHE D 65 TRP 0.017 0.002 TRP M 185 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.52 (19408) covalent geometry : angle 0.79190 / 0.68 (27915) hydrogen bonds : bond 0.09867 / 6.57 ( 1096) hydrogen bonds : angle 4.33555 / 3.19 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7645 (mt-10) REVERT: E 123 ASP cc_start: 0.8714 (m-30) cc_final: 0.8467 (m-30) REVERT: G 94 ASN cc_start: 0.9158 (t0) cc_final: 0.8954 (t0) REVERT: H 42 TYR cc_start: 0.8151 (t80) cc_final: 0.7855 (t80) REVERT: M 96 ASN cc_start: 0.8143 (m-40) cc_final: 0.7911 (m-40) REVERT: M 160 LEU cc_start: 0.8575 (mm) cc_final: 0.8307 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.8255 time to fit residues: 241.3467 Evaluate side-chains 205 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 84 ASN F 93 GLN G 24 GLN H 47 GLN M 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104034 restraints weight = 22345.929| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.30 r_work: 0.3155 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19408 Z= 0.253 Angle : 0.782 8.685 27915 Z= 0.422 Chirality : 0.055 0.262 3152 Planarity : 0.006 0.048 2154 Dihedral : 31.154 172.264 5711 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.83 % Allowed : 11.23 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.23), residues: 1271 helix: 2.27 (0.21), residues: 586 sheet: 0.68 (0.33), residues: 262 loop : -0.42 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.042 0.002 TYR N 201 PHE 0.010 0.002 PHE N 81 TRP 0.017 0.002 TRP M 185 HIS 0.007 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (19408) covalent geometry : angle 0.78177 / 0.42 (27915) hydrogen bonds : bond 0.05952 / 3.95 ( 1096) hydrogen bonds : angle 3.65982 / 2.70 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.497 Fit side-chains REVERT: A 64 LYS cc_start: 0.8855 (mptt) cc_final: 0.8581 (mtpt) REVERT: A 76 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: B 95 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8292 (mtt-85) REVERT: D 79 ARG cc_start: 0.8372 (mtm180) cc_final: 0.8150 (mtp180) REVERT: D 85 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8328 (mttp) REVERT: E 122 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8419 (ptmm) REVERT: F 95 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7964 (mtp-110) REVERT: G 94 ASN cc_start: 0.9371 (t0) cc_final: 0.9134 (t0) REVERT: H 79 ARG cc_start: 0.8488 (mtp180) cc_final: 0.8191 (mtp180) REVERT: M 96 ASN cc_start: 0.8561 (m-40) cc_final: 0.8204 (m-40) REVERT: M 160 LEU cc_start: 0.8598 (mm) cc_final: 0.8262 (mm) REVERT: N 191 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8284 (ptm160) REVERT: N 230 MET cc_start: 0.8818 (ttt) cc_final: 0.8503 (ttt) outliers start: 31 outliers final: 16 residues processed: 224 average time/residue: 0.7719 time to fit residues: 188.0632 Evaluate side-chains 211 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 130 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107005 restraints weight = 22558.687| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.27 r_work: 0.3197 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19408 Z= 0.143 Angle : 0.668 7.804 27915 Z= 0.370 Chirality : 0.048 0.278 3152 Planarity : 0.004 0.039 2154 Dihedral : 31.056 168.127 5711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.37 % Allowed : 12.97 % Favored : 84.66 % 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: 1.86 (0.23), residues: 1271 helix: 2.53 (0.21), residues: 586 sheet: 0.69 (0.33), residues: 262 loop : -0.26 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.016 0.001 TYR N 201 PHE 0.007 0.001 PHE A 67 TRP 0.010 0.001 TRP M 185 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (19408) covalent geometry : angle 0.66780 / 0.37 (27915) hydrogen bonds : bond 0.04164 / 2.77 ( 1096) hydrogen bonds : angle 3.38071 / 2.49 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.464 Fit side-chains REVERT: A 64 LYS cc_start: 0.8835 (mptt) cc_final: 0.8592 (mtpt) REVERT: B 92 ARG cc_start: 0.8884 (ptm-80) cc_final: 0.8613 (ptm160) REVERT: D 85 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: E 122 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8342 (ptmm) REVERT: E 123 ASP cc_start: 0.9122 (m-30) cc_final: 0.8856 (m-30) REVERT: F 95 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7781 (mtp-110) REVERT: G 64 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: G 94 ASN cc_start: 0.9309 (t0) cc_final: 0.9068 (t0) REVERT: M 96 ASN cc_start: 0.8481 (m-40) cc_final: 0.8135 (m-40) REVERT: M 160 LEU cc_start: 0.8603 (mm) cc_final: 0.8254 (mm) REVERT: N 98 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: N 230 MET cc_start: 0.8760 (ttt) cc_final: 0.8425 (ttt) outliers start: 26 outliers final: 10 residues processed: 210 average time/residue: 0.7804 time to fit residues: 178.0304 Evaluate side-chains 201 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 149 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 113 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104166 restraints weight = 22463.523| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.29 r_work: 0.3158 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19408 Z= 0.199 Angle : 0.675 7.330 27915 Z= 0.373 Chirality : 0.048 0.299 3152 Planarity : 0.005 0.043 2154 Dihedral : 30.916 166.565 5711 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.29 % Allowed : 13.42 % Favored : 83.29 % 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: 1.81 (0.23), residues: 1271 helix: 2.51 (0.21), residues: 586 sheet: 0.69 (0.33), residues: 262 loop : -0.33 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.018 0.002 TYR N 201 PHE 0.007 0.001 PHE A 67 TRP 0.010 0.001 TRP M 185 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (19408) covalent geometry : angle 0.67544 / 0.37 (27915) hydrogen bonds : bond 0.05050 / 3.35 ( 1096) hydrogen bonds : angle 3.35816 / 2.47 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8900 (mptt) cc_final: 0.8656 (mtpt) REVERT: A 76 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: B 92 ARG cc_start: 0.8882 (ptm-80) cc_final: 0.8604 (ptm160) REVERT: E 122 LYS cc_start: 0.8597 (ptpp) cc_final: 0.8339 (ptmm) REVERT: F 95 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7852 (mtp-110) REVERT: G 94 ASN cc_start: 0.9329 (t0) cc_final: 0.9087 (t0) REVERT: H 79 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8107 (mtp180) REVERT: M 96 ASN cc_start: 0.8519 (m-40) cc_final: 0.8169 (m-40) REVERT: M 160 LEU cc_start: 0.8621 (mm) cc_final: 0.8253 (mm) REVERT: N 230 MET cc_start: 0.8832 (ttt) cc_final: 0.8425 (ttt) outliers start: 36 outliers final: 20 residues processed: 210 average time/residue: 0.7644 time to fit residues: 174.8266 Evaluate side-chains 207 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 160 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121403 restraints weight = 23967.765| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.39 r_work: 0.3441 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19408 Z= 0.200 Angle : 0.665 6.920 27915 Z= 0.366 Chirality : 0.047 0.281 3152 Planarity : 0.005 0.043 2154 Dihedral : 30.813 163.621 5711 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.20 % Allowed : 14.79 % Favored : 82.01 % 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: 1.73 (0.23), residues: 1271 helix: 2.43 (0.21), residues: 588 sheet: 0.69 (0.33), residues: 262 loop : -0.39 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.019 0.002 TYR N 201 PHE 0.008 0.001 PHE A 78 TRP 0.009 0.001 TRP M 185 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (19408) covalent geometry : angle 0.66525 / 0.37 (27915) hydrogen bonds : bond 0.04557 / 3.02 ( 1096) hydrogen bonds : angle 3.31857 / 2.45 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.466 Fit side-chains REVERT: A 64 LYS cc_start: 0.8893 (mptt) cc_final: 0.8660 (mtpt) REVERT: A 76 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: B 92 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8605 (ptm160) REVERT: C 36 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8160 (mppt) REVERT: C 73 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (t160) REVERT: D 79 ARG cc_start: 0.8413 (mtt90) cc_final: 0.8200 (mtp180) REVERT: D 85 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8418 (mppt) REVERT: E 122 LYS cc_start: 0.8694 (ptpp) cc_final: 0.8468 (ptmm) REVERT: F 95 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7731 (mtp-110) REVERT: G 64 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: G 94 ASN cc_start: 0.9329 (t0) cc_final: 0.9078 (t0) REVERT: M 96 ASN cc_start: 0.8550 (m-40) cc_final: 0.8195 (m-40) REVERT: M 159 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8007 (mm-30) REVERT: M 160 LEU cc_start: 0.8609 (mm) cc_final: 0.8238 (mm) REVERT: M 165 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7839 (p) REVERT: N 230 MET cc_start: 0.8747 (ttt) cc_final: 0.8408 (ttt) outliers start: 35 outliers final: 18 residues processed: 211 average time/residue: 0.7757 time to fit residues: 178.3393 Evaluate side-chains 213 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120761 restraints weight = 23055.057| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.22 r_work: 0.3456 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19408 Z= 0.137 Angle : 0.636 7.606 27915 Z= 0.353 Chirality : 0.045 0.273 3152 Planarity : 0.004 0.053 2154 Dihedral : 30.734 163.771 5711 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 15.71 % Favored : 81.37 % 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: 1.89 (0.24), residues: 1271 helix: 2.60 (0.21), residues: 588 sheet: 0.68 (0.33), residues: 262 loop : -0.31 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.013 0.002 TYR H 42 PHE 0.007 0.001 PHE A 67 TRP 0.009 0.001 TRP M 185 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (19408) covalent geometry : angle 0.63556 / 0.35 (27915) hydrogen bonds : bond 0.04099 / 2.72 ( 1096) hydrogen bonds : angle 3.25082 / 2.39 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8853 (mptt) cc_final: 0.8611 (mtpt) REVERT: A 76 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: B 92 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8532 (ptm160) REVERT: C 73 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (t160) REVERT: E 122 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8410 (ptmm) REVERT: F 95 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7624 (mtp-110) REVERT: G 13 LYS cc_start: 0.8579 (tptm) cc_final: 0.8376 (tmtt) REVERT: G 74 LYS cc_start: 0.8854 (mppt) cc_final: 0.8571 (mmtp) REVERT: G 94 ASN cc_start: 0.9292 (t0) cc_final: 0.9048 (t0) REVERT: H 76 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: M 96 ASN cc_start: 0.8486 (m-40) cc_final: 0.8100 (m-40) REVERT: M 159 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: M 160 LEU cc_start: 0.8599 (mm) cc_final: 0.8217 (mm) REVERT: N 230 MET cc_start: 0.8718 (ttt) cc_final: 0.8359 (ttt) outliers start: 32 outliers final: 16 residues processed: 206 average time/residue: 0.7990 time to fit residues: 179.2919 Evaluate side-chains 209 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 122 optimal weight: 0.0000 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120646 restraints weight = 23275.453| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.25 r_work: 0.3459 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19408 Z= 0.146 Angle : 0.611 6.659 27915 Z= 0.343 Chirality : 0.044 0.270 3152 Planarity : 0.004 0.049 2154 Dihedral : 30.484 163.487 5711 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.01 % Allowed : 15.62 % Favored : 81.37 % 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: 2.03 (0.24), residues: 1271 helix: 2.70 (0.21), residues: 586 sheet: 0.74 (0.33), residues: 262 loop : -0.18 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 33 TYR 0.017 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (19408) covalent geometry : angle 0.61124 / 0.34 (27915) hydrogen bonds : bond 0.03982 / 2.64 ( 1096) hydrogen bonds : angle 3.15511 / 2.32 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8879 (mptt) cc_final: 0.8646 (mtpt) REVERT: A 76 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: B 74 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7833 (mt-10) REVERT: B 92 ARG cc_start: 0.8873 (ptm-80) cc_final: 0.8560 (ptm160) REVERT: E 120 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7716 (mtt) REVERT: F 95 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7678 (mtp-110) REVERT: G 73 ASN cc_start: 0.7853 (m110) cc_final: 0.7581 (t160) REVERT: G 94 ASN cc_start: 0.9238 (t0) cc_final: 0.8978 (t0) REVERT: M 96 ASN cc_start: 0.8520 (m-40) cc_final: 0.8147 (m-40) REVERT: M 159 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: N 230 MET cc_start: 0.8720 (ttt) cc_final: 0.8388 (ttt) outliers start: 33 outliers final: 20 residues processed: 211 average time/residue: 0.8122 time to fit residues: 186.8182 Evaluate side-chains 209 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 108 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 10.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.166656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120690 restraints weight = 23141.939| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.21 r_work: 0.3459 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19408 Z= 0.158 Angle : 0.617 6.738 27915 Z= 0.345 Chirality : 0.044 0.277 3152 Planarity : 0.004 0.057 2154 Dihedral : 30.453 163.064 5711 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.47 % Allowed : 16.71 % Favored : 80.82 % 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: 1.99 (0.24), residues: 1271 helix: 2.66 (0.21), residues: 586 sheet: 0.71 (0.33), residues: 262 loop : -0.19 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 33 TYR 0.018 0.002 TYR D 40 PHE 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (19408) covalent geometry : angle 0.61680 / 0.35 (27915) hydrogen bonds : bond 0.04121 / 2.74 ( 1096) hydrogen bonds : angle 3.18466 / 2.34 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8879 (mptt) cc_final: 0.8643 (mtpt) REVERT: A 76 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: B 74 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7810 (mt-10) REVERT: B 92 ARG cc_start: 0.8875 (ptm-80) cc_final: 0.8555 (ptm160) REVERT: B 95 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8050 (mtt-85) REVERT: F 95 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7674 (mtp-110) REVERT: G 73 ASN cc_start: 0.7877 (m110) cc_final: 0.7629 (t160) REVERT: G 94 ASN cc_start: 0.9266 (t0) cc_final: 0.8939 (t0) REVERT: M 96 ASN cc_start: 0.8512 (m-40) cc_final: 0.8146 (m-40) REVERT: M 159 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: M 160 LEU cc_start: 0.8600 (mm) cc_final: 0.8154 (mm) REVERT: N 230 MET cc_start: 0.8744 (ttt) cc_final: 0.8394 (ttt) outliers start: 27 outliers final: 21 residues processed: 205 average time/residue: 0.7826 time to fit residues: 174.9712 Evaluate side-chains 212 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 103 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 26 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.166204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117637 restraints weight = 24181.856| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.30 r_work: 0.3411 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19408 Z= 0.249 Angle : 0.674 7.378 27915 Z= 0.370 Chirality : 0.047 0.306 3152 Planarity : 0.005 0.053 2154 Dihedral : 30.549 161.591 5711 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.92 % Allowed : 16.44 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.23), residues: 1271 helix: 2.41 (0.21), residues: 586 sheet: 0.61 (0.32), residues: 262 loop : -0.35 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 33 TYR 0.019 0.002 TYR D 40 PHE 0.010 0.002 PHE C 25 TRP 0.009 0.002 TRP M 185 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (19408) covalent geometry : angle 0.67425 / 0.37 (27915) hydrogen bonds : bond 0.05355 / 3.56 ( 1096) hydrogen bonds : angle 3.32778 / 2.45 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8905 (mptt) cc_final: 0.8663 (mtpt) REVERT: A 76 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: B 74 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7836 (mt-10) REVERT: B 79 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7733 (mtpt) REVERT: B 92 ARG cc_start: 0.8930 (ptm-80) cc_final: 0.8582 (ptm160) REVERT: B 95 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8076 (mtt-85) REVERT: D 85 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8426 (mppt) REVERT: F 95 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7707 (mtp-110) REVERT: G 73 ASN cc_start: 0.7957 (m110) cc_final: 0.7650 (t160) REVERT: G 94 ASN cc_start: 0.9344 (t0) cc_final: 0.9082 (t0) REVERT: M 96 ASN cc_start: 0.8527 (m-40) cc_final: 0.8202 (m-40) REVERT: M 159 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: N 230 MET cc_start: 0.8827 (ttt) cc_final: 0.8476 (ttt) outliers start: 32 outliers final: 16 residues processed: 207 average time/residue: 0.7613 time to fit residues: 171.7775 Evaluate side-chains 210 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 90 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.118908 restraints weight = 24290.347| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.31 r_work: 0.3429 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19408 Z= 0.155 Angle : 0.647 8.065 27915 Z= 0.358 Chirality : 0.045 0.292 3152 Planarity : 0.005 0.065 2154 Dihedral : 30.543 161.884 5711 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 17.63 % Favored : 80.27 % 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: 1.81 (0.24), residues: 1271 helix: 2.52 (0.21), residues: 586 sheet: 0.60 (0.33), residues: 262 loop : -0.28 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 33 TYR 0.020 0.002 TYR D 40 PHE 0.007 0.001 PHE A 67 TRP 0.010 0.001 TRP M 185 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (19408) covalent geometry : angle 0.64743 / 0.36 (27915) hydrogen bonds : bond 0.04634 / 3.08 ( 1096) hydrogen bonds : angle 3.30037 / 2.42 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8870 (mptt) cc_final: 0.8626 (mtpt) REVERT: A 76 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: B 74 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7820 (mt-10) REVERT: B 79 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.7731 (mtpt) REVERT: B 92 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8551 (ptm160) REVERT: B 95 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8005 (mtt-85) REVERT: F 95 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7613 (mtp-110) REVERT: G 73 ASN cc_start: 0.7923 (m110) cc_final: 0.7631 (t160) REVERT: G 94 ASN cc_start: 0.9328 (t0) cc_final: 0.9067 (t0) REVERT: M 96 ASN cc_start: 0.8501 (m-40) cc_final: 0.8120 (m-40) REVERT: M 159 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: N 230 MET cc_start: 0.8785 (ttt) cc_final: 0.8443 (ttt) outliers start: 23 outliers final: 17 residues processed: 209 average time/residue: 0.7749 time to fit residues: 176.4084 Evaluate side-chains 210 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 119 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 150 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120403 restraints weight = 23255.757| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.23 r_work: 0.3449 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19408 Z= 0.137 Angle : 0.624 6.948 27915 Z= 0.347 Chirality : 0.044 0.291 3152 Planarity : 0.004 0.063 2154 Dihedral : 30.480 160.499 5711 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 17.99 % Favored : 80.27 % 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: 1.92 (0.24), residues: 1271 helix: 2.62 (0.21), residues: 586 sheet: 0.64 (0.33), residues: 262 loop : -0.22 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 33 TYR 0.017 0.001 TYR D 40 PHE 0.007 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (19408) covalent geometry : angle 0.62367 / 0.35 (27915) hydrogen bonds : bond 0.04036 / 2.68 ( 1096) hydrogen bonds : angle 3.23813 / 2.37 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8004.10 seconds wall clock time: 136 minutes 21.10 seconds (8181.10 seconds total)