Starting phenix.real_space_refine on Sun Sep 13 01:00:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k60_22685/09_2026/7k60_22685.map" } resolution = 3.12 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= -0.000 sd= 1.000 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 10288 2.51 5 N 3355 2.21 5 O 4261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 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: 18330 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: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 607 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 3.64, per 1000 atoms: 0.20 Number of scatterers: 18330 At special positions: 0 Unit cell: (136.68, 123.28, 198.32, 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 4261 8.00 N 3355 7.00 C 10288 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: 1.56 Conformation dependent library (CDL) restraints added in 433.3 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 23 sheets defined 48.6% alpha, 21.0% beta 197 base pairs and 330 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.723A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.551A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) 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 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.611A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.538A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.153A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (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 124 removed outlier: 3.534A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.614A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.669A 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 74 removed outlier: 4.189A 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 removed outlier: 3.762A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.640A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) 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 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: 3.906A 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 45 through 59 removed outlier: 3.884A pdb=" N ARG U 56 " --> pdb=" O VAL U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 74 Processing helix chain 'U' and resid 83 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.758A 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: 7.365A 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: 6.559A 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: 6.726A 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: 7.352A 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: 3.786A 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: 6.653A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.507A 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 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: 6.345A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS M 208 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.345A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.952A 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 24 removed outlier: 3.839A 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: 6.608A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.458A 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: 7.932A pdb=" N TYR N 181 " --> pdb=" O TYR N 201 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR N 201 " --> pdb=" O TYR N 181 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.866A 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: 3.955A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.805A pdb=" N SER U 112 " --> pdb=" O VAL U 104 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 330 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.09 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: 2773 1.33 - 1.45: 6782 1.45 - 1.57: 9093 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19486 Sorted by residual: bond pdb=" C3' DT J 165 " pdb=" C2' DT J 165 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J 120 " pdb=" C2' DG J 120 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 197 " pdb=" C2' DC I 197 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DA I 122 " pdb=" C2' DA I 122 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 bond pdb=" C3' DG I 171 " pdb=" C2' DG I 171 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 ... (remaining 19481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 26596 1.75 - 3.51: 1363 3.51 - 5.26: 55 5.26 - 7.01: 8 7.01 - 8.77: 1 Bond angle restraints: 28023 Sorted by residual: angle pdb=" O4' DC J 71 " pdb=" C4' DC J 71 " pdb=" C3' DC J 71 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT I 180 " pdb=" C4 DT I 180 " pdb=" O4 DT I 180 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 111 " pdb=" C4 DT I 111 " pdb=" O4 DT I 111 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 102 " pdb=" C4 DT I 102 " pdb=" O4 DT I 102 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT J 19 " pdb=" C4 DT J 19 " pdb=" O4 DT J 19 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 28018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 8722 34.38 - 68.75: 1886 68.75 - 103.13: 28 103.13 - 137.51: 0 137.51 - 171.89: 2 Dihedral angle restraints: 10638 sinusoidal: 6875 harmonic: 3763 Sorted by residual: 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 48.11 171.89 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 74.51 145.49 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA TYR N 106 " pdb=" C TYR N 106 " pdb=" N CYS N 107 " pdb=" CA CYS N 107 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 10635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1974 0.038 - 0.076: 834 0.076 - 0.114: 283 0.114 - 0.152: 57 0.152 - 0.189: 6 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CB THR N 177 " pdb=" CA THR N 177 " pdb=" OG1 THR N 177 " pdb=" CG2 THR N 177 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA LYS F 31 " pdb=" N LYS F 31 " pdb=" C LYS F 31 " pdb=" CB LYS F 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 3151 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 40 " 0.014 2.00e-02 2.50e+03 1.69e-02 5.72e+00 pdb=" CG TYR D 40 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR D 40 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 40 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 40 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 40 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 40 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 201 " -0.017 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR N 201 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR N 201 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR N 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR N 201 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 201 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR N 201 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 201 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 66 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.028 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1085 2.72 - 3.27: 16996 3.27 - 3.81: 35484 3.81 - 4.36: 43449 4.36 - 4.90: 63293 Nonbonded interactions: 160307 Sorted by model distance: nonbonded pdb=" NH2 ARG N 80 " pdb=" O ASN N 96 " model vdw 2.175 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR M 55 " pdb=" OG1 THR M 255 " model vdw 2.182 3.040 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.219 3.040 ... (remaining 160302 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: 0.990 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.600 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 0.052 19486 Z= 0.499 Angle : 0.780 8.767 28023 Z= 0.660 Chirality : 0.046 0.189 3154 Planarity : 0.004 0.050 2171 Dihedral : 26.554 171.886 8228 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % 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: 0.43 (0.23), residues: 1272 helix: 1.02 (0.20), residues: 590 sheet: 0.43 (0.34), residues: 238 loop : -0.68 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 37 TYR 0.041 0.002 TYR D 40 PHE 0.013 0.002 PHE C 25 TRP 0.020 0.003 TRP M 60 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.50 (19486) covalent geometry : angle 0.78031 / 0.66 (28023) hydrogen bonds : bond 0.10404 / 7.15 ( 1102) hydrogen bonds : angle 4.44198 / 3.29 ( 2709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7284 (mmp) cc_final: 0.7021 (mmp) REVERT: A 94 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6769 (mm-30) REVERT: B 95 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7628 (mpt180) REVERT: D 59 MET cc_start: 0.7018 (tpp) cc_final: 0.6096 (tpt) REVERT: D 67 ASN cc_start: 0.8173 (m-40) cc_final: 0.7951 (m110) REVERT: G 90 ASP cc_start: 0.6586 (t0) cc_final: 0.6304 (t0) REVERT: N 229 TYR cc_start: 0.6648 (m-80) cc_final: 0.6434 (m-80) REVERT: N 238 GLU cc_start: 0.7589 (tt0) cc_final: 0.7352 (pt0) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1487 time to fit residues: 53.7186 Evaluate side-chains 188 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 95 ASN U 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117382 restraints weight = 30065.203| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.88 r_work: 0.3393 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19486 Z= 0.261 Angle : 0.758 11.607 28023 Z= 0.427 Chirality : 0.051 0.278 3154 Planarity : 0.006 0.050 2171 Dihedral : 30.339 173.885 5718 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.45 % Allowed : 9.34 % Favored : 89.21 % 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: 0.06 (0.22), residues: 1272 helix: 0.62 (0.20), residues: 588 sheet: 0.43 (0.34), residues: 230 loop : -0.82 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.029 0.003 TYR B 88 PHE 0.015 0.002 PHE C 25 TRP 0.019 0.003 TRP M 196 HIS 0.007 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 (19486) covalent geometry : angle 0.75752 / 0.43 (28023) hydrogen bonds : bond 0.05705 / 3.91 ( 1102) hydrogen bonds : angle 3.96653 / 2.93 ( 2709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 95 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7976 (mpt180) REVERT: D 59 MET cc_start: 0.7306 (tpp) cc_final: 0.6784 (tpt) REVERT: E 42 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6988 (ttm-80) REVERT: E 50 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7801 (mt-10) REVERT: E 112 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8661 (mp) REVERT: H 34 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8007 (mtmm) REVERT: M 21 ILE cc_start: 0.7949 (mp) cc_final: 0.7721 (mp) REVERT: M 230 MET cc_start: 0.6260 (ttp) cc_final: 0.5977 (ttp) REVERT: N 36 GLU cc_start: 0.7820 (pt0) cc_final: 0.6811 (pm20) REVERT: N 80 ARG cc_start: 0.6760 (ptm-80) cc_final: 0.6530 (ptm-80) REVERT: N 101 ASP cc_start: 0.6261 (m-30) cc_final: 0.5704 (m-30) REVERT: N 238 GLU cc_start: 0.7994 (tt0) cc_final: 0.7330 (pt0) outliers start: 16 outliers final: 10 residues processed: 203 average time/residue: 0.1595 time to fit residues: 47.4166 Evaluate side-chains 187 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain N residue 186 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 47 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 92 optimal weight: 50.0000 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.165538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118192 restraints weight = 30146.767| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.81 r_work: 0.3387 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19486 Z= 0.187 Angle : 0.677 8.969 28023 Z= 0.388 Chirality : 0.047 0.305 3154 Planarity : 0.005 0.046 2171 Dihedral : 30.420 176.504 5718 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.36 % Allowed : 11.33 % Favored : 86.31 % 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: 0.38 (0.23), residues: 1272 helix: 1.06 (0.21), residues: 588 sheet: 0.35 (0.34), residues: 230 loop : -0.78 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 116 TYR 0.021 0.002 TYR B 88 PHE 0.011 0.002 PHE C 25 TRP 0.032 0.003 TRP M 60 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (19486) covalent geometry : angle 0.67670 / 0.39 (28023) hydrogen bonds : bond 0.04669 / 3.21 ( 1102) hydrogen bonds : angle 3.71534 / 2.73 ( 2709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.462 Fit side-chains REVERT: A 87 SER cc_start: 0.7702 (t) cc_final: 0.7477 (p) REVERT: A 94 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 95 ARG cc_start: 0.8199 (mmt-90) cc_final: 0.7933 (mpt180) REVERT: D 42 TYR cc_start: 0.7995 (t80) cc_final: 0.7406 (t80) REVERT: D 59 MET cc_start: 0.7217 (tpp) cc_final: 0.6895 (tpt) REVERT: E 50 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7907 (mt-10) REVERT: E 112 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8767 (mp) REVERT: H 34 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7927 (mtmm) REVERT: M 21 ILE cc_start: 0.8002 (mp) cc_final: 0.7761 (mp) REVERT: M 98 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7899 (tp30) REVERT: M 219 LEU cc_start: 0.6528 (mt) cc_final: 0.6269 (mp) REVERT: M 232 LEU cc_start: 0.8002 (mt) cc_final: 0.7749 (mt) REVERT: M 238 GLU cc_start: 0.7448 (pt0) cc_final: 0.6910 (pm20) REVERT: N 36 GLU cc_start: 0.7552 (pt0) cc_final: 0.6681 (pm20) REVERT: N 80 ARG cc_start: 0.6801 (ptm-80) cc_final: 0.6534 (ptm-80) REVERT: N 98 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7947 (mt-10) REVERT: N 101 ASP cc_start: 0.6459 (m-30) cc_final: 0.6052 (m-30) REVERT: N 238 GLU cc_start: 0.7906 (tt0) cc_final: 0.7309 (pt0) outliers start: 26 outliers final: 17 residues processed: 211 average time/residue: 0.1390 time to fit residues: 44.3866 Evaluate side-chains 203 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain N residue 218 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 245 CYS 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 63 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.166712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119823 restraints weight = 30105.698| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.80 r_work: 0.3395 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19486 Z= 0.149 Angle : 0.643 9.375 28023 Z= 0.370 Chirality : 0.045 0.293 3154 Planarity : 0.004 0.043 2171 Dihedral : 30.364 176.298 5718 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.99 % Allowed : 14.23 % Favored : 83.77 % 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: 0.79 (0.23), residues: 1272 helix: 1.44 (0.21), residues: 588 sheet: 0.50 (0.33), residues: 230 loop : -0.60 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.018 0.002 TYR D 40 PHE 0.008 0.001 PHE C 25 TRP 0.021 0.002 TRP M 60 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (19486) covalent geometry : angle 0.64311 / 0.37 (28023) hydrogen bonds : bond 0.04278 / 2.95 ( 1102) hydrogen bonds : angle 3.54863 / 2.60 ( 2709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7599 (t) cc_final: 0.7373 (p) REVERT: A 94 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 95 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7821 (mpt180) REVERT: D 42 TYR cc_start: 0.7839 (t80) cc_final: 0.7490 (t80) REVERT: E 50 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7611 (mt-10) REVERT: E 112 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8459 (mp) REVERT: H 34 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7891 (mtmm) REVERT: M 21 ILE cc_start: 0.8047 (mp) cc_final: 0.7770 (mp) REVERT: M 98 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8029 (tp30) REVERT: M 238 GLU cc_start: 0.7020 (pt0) cc_final: 0.6652 (pm20) REVERT: N 23 MET cc_start: 0.8052 (mmp) cc_final: 0.7599 (mmp) REVERT: N 98 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7679 (mt-10) REVERT: N 238 GLU cc_start: 0.7757 (tt0) cc_final: 0.7314 (pt0) outliers start: 22 outliers final: 13 residues processed: 210 average time/residue: 0.1507 time to fit residues: 47.0642 Evaluate side-chains 190 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 245 CYS 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 145 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN M 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.166468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.119715 restraints weight = 30079.501| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.80 r_work: 0.3411 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19486 Z= 0.156 Angle : 0.642 11.195 28023 Z= 0.368 Chirality : 0.045 0.287 3154 Planarity : 0.004 0.042 2171 Dihedral : 30.365 176.432 5718 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.08 % Allowed : 14.23 % Favored : 82.68 % 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: 0.79 (0.23), residues: 1272 helix: 1.41 (0.21), residues: 588 sheet: 0.51 (0.33), residues: 230 loop : -0.57 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.032 0.002 TYR D 40 PHE 0.009 0.001 PHE C 25 TRP 0.028 0.002 TRP M 60 HIS 0.004 0.001 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (19486) covalent geometry : angle 0.64152 / 0.37 (28023) hydrogen bonds : bond 0.04307 / 2.97 ( 1102) hydrogen bonds : angle 3.52617 / 2.57 ( 2709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7616 (t) cc_final: 0.7391 (p) REVERT: A 94 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 95 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7894 (mpt180) REVERT: D 42 TYR cc_start: 0.7990 (t80) cc_final: 0.7528 (t80) REVERT: E 50 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7887 (mt-10) REVERT: E 112 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8433 (mp) REVERT: H 34 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7933 (mtmm) REVERT: M 21 ILE cc_start: 0.8005 (mp) cc_final: 0.7733 (mp) REVERT: M 98 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7953 (tp30) REVERT: M 238 GLU cc_start: 0.7014 (pt0) cc_final: 0.6655 (pm20) REVERT: N 23 MET cc_start: 0.8205 (mmp) cc_final: 0.7755 (mmp) REVERT: N 80 ARG cc_start: 0.6956 (ptm-80) cc_final: 0.6694 (ptm-80) REVERT: N 101 ASP cc_start: 0.6262 (m-30) cc_final: 0.5704 (m-30) REVERT: N 238 GLU cc_start: 0.7795 (tt0) cc_final: 0.7384 (pt0) outliers start: 34 outliers final: 22 residues processed: 210 average time/residue: 0.1432 time to fit residues: 45.5319 Evaluate side-chains 202 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR 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 78 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN ** F 93 GLN ** 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 = 0.4325 r_free = 0.4325 target = 0.166484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.119580 restraints weight = 30016.763| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.95 r_work: 0.3397 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19486 Z= 0.153 Angle : 0.641 13.073 28023 Z= 0.366 Chirality : 0.044 0.286 3154 Planarity : 0.004 0.042 2171 Dihedral : 30.367 176.978 5718 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.90 % Allowed : 14.87 % Favored : 82.23 % 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: 0.84 (0.23), residues: 1272 helix: 1.47 (0.21), residues: 588 sheet: 0.52 (0.33), residues: 230 loop : -0.56 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 37 TYR 0.026 0.001 TYR D 40 PHE 0.010 0.001 PHE C 25 TRP 0.027 0.002 TRP M 60 HIS 0.007 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (19486) covalent geometry : angle 0.64096 / 0.37 (28023) hydrogen bonds : bond 0.04248 / 2.94 ( 1102) hydrogen bonds : angle 3.50013 / 2.56 ( 2709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7611 (t) cc_final: 0.7381 (p) REVERT: A 94 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 95 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7871 (mpt180) REVERT: D 42 TYR cc_start: 0.7889 (t80) cc_final: 0.7435 (t80) REVERT: E 50 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7886 (mt-10) REVERT: E 112 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8422 (mp) REVERT: H 34 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7910 (mtmm) REVERT: M 21 ILE cc_start: 0.8139 (mp) cc_final: 0.7863 (mp) REVERT: M 98 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7918 (tp30) REVERT: M 238 GLU cc_start: 0.7098 (pt0) cc_final: 0.6660 (pm20) REVERT: N 101 ASP cc_start: 0.6330 (m-30) cc_final: 0.5876 (m-30) REVERT: N 238 GLU cc_start: 0.7790 (tt0) cc_final: 0.7357 (pt0) REVERT: U 80 ASP cc_start: 0.6874 (t0) cc_final: 0.6474 (t0) outliers start: 32 outliers final: 21 residues processed: 206 average time/residue: 0.1467 time to fit residues: 45.5557 Evaluate side-chains 198 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR 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 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 11 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121138 restraints weight = 30177.041| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.91 r_work: 0.3448 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19486 Z= 0.129 Angle : 0.618 14.082 28023 Z= 0.355 Chirality : 0.043 0.285 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.289 177.560 5718 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 15.68 % Favored : 82.14 % 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: 1.13 (0.23), residues: 1272 helix: 1.78 (0.21), residues: 588 sheet: 0.56 (0.33), residues: 230 loop : -0.48 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 37 TYR 0.029 0.001 TYR D 40 PHE 0.009 0.001 PHE D 65 TRP 0.034 0.002 TRP M 60 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (19486) covalent geometry : angle 0.61830 / 0.35 (28023) hydrogen bonds : bond 0.03911 / 2.72 ( 1102) hydrogen bonds : angle 3.38866 / 2.48 ( 2709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 95 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7825 (mpt180) REVERT: D 42 TYR cc_start: 0.8026 (t80) cc_final: 0.7667 (t80) REVERT: E 50 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7800 (mt-10) REVERT: E 112 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8251 (mp) REVERT: H 34 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7791 (mtmm) REVERT: M 21 ILE cc_start: 0.8099 (mp) cc_final: 0.7693 (mp) REVERT: M 98 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7871 (tp30) REVERT: M 238 GLU cc_start: 0.6993 (pt0) cc_final: 0.6551 (pm20) REVERT: N 36 GLU cc_start: 0.7546 (pt0) cc_final: 0.6382 (pm20) REVERT: N 238 GLU cc_start: 0.7637 (tt0) cc_final: 0.7294 (pt0) REVERT: U 80 ASP cc_start: 0.6906 (t0) cc_final: 0.6488 (t0) outliers start: 24 outliers final: 18 residues processed: 208 average time/residue: 0.1499 time to fit residues: 46.5778 Evaluate side-chains 200 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 245 CYS 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 28 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 109 optimal weight: 50.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 63 ASN ** G 73 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 = 0.4341 r_free = 0.4341 target = 0.167752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120833 restraints weight = 30167.516| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.96 r_work: 0.3440 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19486 Z= 0.136 Angle : 0.621 13.680 28023 Z= 0.355 Chirality : 0.043 0.278 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.272 177.551 5718 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 16.23 % Favored : 81.50 % 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: 1.17 (0.23), residues: 1272 helix: 1.84 (0.21), residues: 588 sheet: 0.56 (0.33), residues: 230 loop : -0.47 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 45 TYR 0.025 0.001 TYR D 40 PHE 0.008 0.001 PHE C 25 TRP 0.032 0.002 TRP M 60 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (19486) covalent geometry : angle 0.62053 / 0.36 (28023) hydrogen bonds : bond 0.04000 / 2.78 ( 1102) hydrogen bonds : angle 3.38373 / 2.47 ( 2709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 95 ARG cc_start: 0.8229 (mmt-90) cc_final: 0.7834 (mpt180) REVERT: D 34 LYS cc_start: 0.8170 (mttm) cc_final: 0.7913 (mttt) REVERT: D 42 TYR cc_start: 0.8072 (t80) cc_final: 0.7644 (t80) REVERT: E 50 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7800 (mt-10) REVERT: E 112 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8280 (mp) REVERT: H 34 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7850 (mtmm) REVERT: M 98 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7890 (tp30) REVERT: M 238 GLU cc_start: 0.6980 (pt0) cc_final: 0.6557 (pm20) REVERT: N 36 GLU cc_start: 0.7650 (pt0) cc_final: 0.6423 (pm20) REVERT: N 238 GLU cc_start: 0.7634 (tt0) cc_final: 0.7403 (pt0) REVERT: U 80 ASP cc_start: 0.7127 (t0) cc_final: 0.6727 (t0) outliers start: 25 outliers final: 20 residues processed: 197 average time/residue: 0.1459 time to fit residues: 43.6594 Evaluate side-chains 196 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 207 THR 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 122 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 137 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 63 ASN ** G 73 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 = 0.4352 r_free = 0.4352 target = 0.168595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121323 restraints weight = 30039.501| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.96 r_work: 0.3457 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19486 Z= 0.128 Angle : 0.608 14.238 28023 Z= 0.350 Chirality : 0.042 0.278 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.225 178.567 5718 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.27 % Allowed : 16.86 % Favored : 80.87 % 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: 1.27 (0.23), residues: 1272 helix: 1.92 (0.21), residues: 592 sheet: 0.51 (0.33), residues: 240 loop : -0.40 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.028 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.034 0.002 TRP M 60 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (19486) covalent geometry : angle 0.60792 / 0.35 (28023) hydrogen bonds : bond 0.03870 / 2.68 ( 1102) hydrogen bonds : angle 3.31877 / 2.42 ( 2709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8236 (mmt-90) cc_final: 0.7848 (mpt180) REVERT: D 42 TYR cc_start: 0.8110 (t80) cc_final: 0.7762 (t80) REVERT: E 50 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7877 (mt-10) REVERT: E 112 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8222 (mp) REVERT: H 34 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7884 (mtmm) REVERT: M 238 GLU cc_start: 0.6980 (pt0) cc_final: 0.6527 (pm20) REVERT: U 80 ASP cc_start: 0.7151 (t0) cc_final: 0.6746 (t0) outliers start: 25 outliers final: 19 residues processed: 193 average time/residue: 0.1472 time to fit residues: 42.8897 Evaluate side-chains 184 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 207 THR 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 137 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.167279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121396 restraints weight = 30084.894| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.88 r_work: 0.3422 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19486 Z= 0.157 Angle : 0.637 14.002 28023 Z= 0.361 Chirality : 0.043 0.273 3154 Planarity : 0.004 0.040 2171 Dihedral : 30.276 178.730 5718 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.99 % Allowed : 17.32 % Favored : 80.69 % 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: 1.09 (0.23), residues: 1272 helix: 1.73 (0.21), residues: 590 sheet: 0.51 (0.33), residues: 240 loop : -0.47 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 37 TYR 0.029 0.002 TYR D 40 PHE 0.011 0.001 PHE C 25 TRP 0.034 0.002 TRP M 60 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (19486) covalent geometry : angle 0.63704 / 0.36 (28023) hydrogen bonds : bond 0.04254 / 2.92 ( 1102) hydrogen bonds : angle 3.40061 / 2.48 ( 2709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7690 (mm-30) REVERT: B 95 ARG cc_start: 0.8216 (mmt-90) cc_final: 0.7819 (mpt180) REVERT: D 42 TYR cc_start: 0.8185 (t80) cc_final: 0.7681 (t80) REVERT: E 50 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7885 (mt-10) REVERT: E 112 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8348 (mp) REVERT: H 34 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7892 (mtmm) REVERT: M 195 GLU cc_start: 0.7965 (pm20) cc_final: 0.7696 (pm20) REVERT: M 238 GLU cc_start: 0.6981 (pt0) cc_final: 0.6614 (pm20) REVERT: N 238 GLU cc_start: 0.7839 (pt0) cc_final: 0.7194 (pm20) REVERT: U 80 ASP cc_start: 0.6938 (t0) cc_final: 0.6567 (t0) outliers start: 22 outliers final: 20 residues processed: 188 average time/residue: 0.1457 time to fit residues: 41.1297 Evaluate side-chains 193 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 177 THR Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 207 THR 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 127 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** G 73 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 = 0.4341 r_free = 0.4341 target = 0.167761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121352 restraints weight = 30177.668| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.87 r_work: 0.3440 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19486 Z= 0.142 Angle : 0.630 14.437 28023 Z= 0.359 Chirality : 0.043 0.275 3154 Planarity : 0.004 0.057 2171 Dihedral : 30.269 179.689 5718 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.09 % Allowed : 17.50 % Favored : 80.42 % 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: 1.17 (0.23), residues: 1272 helix: 1.81 (0.21), residues: 590 sheet: 0.51 (0.33), residues: 240 loop : -0.44 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 37 TYR 0.029 0.001 TYR D 40 PHE 0.009 0.001 PHE C 25 TRP 0.034 0.002 TRP M 60 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (19486) covalent geometry : angle 0.63033 / 0.36 (28023) hydrogen bonds : bond 0.04084 / 2.81 ( 1102) hydrogen bonds : angle 3.36830 / 2.45 ( 2709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7626.00 seconds wall clock time: 130 minutes 9.86 seconds (7809.86 seconds total)