Starting phenix.real_space_refine on Thu Mar 5 05:48:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.map" model { file = "/net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k63_22687/03_2026/7k63_22687.cif" } resolution = 3.03 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 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.00, per 1000 atoms: 0.22 Number of scatterers: 18330 At special positions: 0 Unit cell: (131.62, 123.643, 196.766, 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: 1.59 Conformation dependent library (CDL) restraints added in 541.5 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 48.8% alpha, 20.6% beta 197 base pairs and 334 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.559A 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 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 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: 3.950A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.156A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) 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: 3.602A 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: 3.567A 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: 4.255A 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 removed outlier: 3.540A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) 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: 3.899A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) 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: 3.709A 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 removed outlier: 3.514A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) 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: 3.717A 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: 3.800A 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: 6.869A 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: 7.067A 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: 6.486A 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: 6.632A 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: 6.996A 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: 3.699A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER M 91 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.500A 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: 3.849A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 32 " --> 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: 6.555A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.892A 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: 3.996A 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 Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.757A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.942A 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: 6.615A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.893A 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: 3.944A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65 617 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 334 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.14 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: 3676 1.33 - 1.45: 6202 1.45 - 1.57: 8770 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19486 Sorted by residual: bond pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CA GLY U 59 " pdb=" C GLY U 59 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 1.442 1.450 -0.009 7.70e-03 1.69e+04 1.26e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CA GLU U 60 " pdb=" C GLU U 60 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.19e+00 ... (remaining 19481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 26867 1.42 - 2.85: 1060 2.85 - 4.27: 73 4.27 - 5.69: 18 5.69 - 7.12: 5 Bond angle restraints: 28023 Sorted by residual: angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 114.65 118.04 -3.39 9.20e-01 1.18e+00 1.36e+01 angle pdb=" CB LYS C 74 " pdb=" CG LYS C 74 " pdb=" CD LYS C 74 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.57e+00 angle pdb=" C3' DC I 72 " pdb=" C2' DC I 72 " pdb=" C1' DC I 72 " ideal model delta sigma weight residual 101.60 97.87 3.73 1.50e+00 4.44e-01 6.17e+00 angle pdb=" C TYR M 69 " pdb=" N ALA M 70 " pdb=" CA ALA M 70 " ideal model delta sigma weight residual 121.54 126.04 -4.50 1.91e+00 2.74e-01 5.56e+00 angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 110.80 115.67 -4.87 2.13e+00 2.20e-01 5.23e+00 ... (remaining 28018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 8763 35.60 - 71.19: 1849 71.19 - 106.79: 24 106.79 - 142.38: 0 142.38 - 177.98: 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 42.02 177.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N ARG A 83 " pdb=" CA ARG A 83 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+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 70.16 149.84 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 10635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2015 0.031 - 0.062: 855 0.062 - 0.093: 194 0.093 - 0.125: 84 0.125 - 0.156: 6 Chirality restraints: 3154 Sorted by residual: chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE N 67 " pdb=" N ILE N 67 " pdb=" C ILE N 67 " pdb=" CB ILE N 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE M 94 " pdb=" N ILE M 94 " pdb=" C ILE M 94 " pdb=" CB ILE M 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3151 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 169 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO M 170 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO M 170 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 170 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 103 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO H 103 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.023 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 861 2.71 - 3.25: 16531 3.25 - 3.80: 35102 3.80 - 4.35: 44424 4.35 - 4.90: 64273 Nonbonded interactions: 161191 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.158 3.040 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG M 251 " model vdw 2.204 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLN M 184 " pdb=" NE1 TRP M 196 " model vdw 2.236 3.120 nonbonded pdb=" OE1 GLU D 71 " pdb=" NZ LYS F 91 " model vdw 2.251 3.120 ... (remaining 161186 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.540 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19486 Z= 0.200 Angle : 0.621 7.116 28023 Z= 0.377 Chirality : 0.037 0.156 3154 Planarity : 0.004 0.057 2171 Dihedral : 26.716 177.979 8228 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.23), residues: 1272 helix: 1.53 (0.21), residues: 592 sheet: 0.23 (0.33), residues: 238 loop : -0.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.022 0.002 TYR G 50 PHE 0.013 0.002 PHE C 25 TRP 0.019 0.002 TRP M 196 HIS 0.005 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00436 (19486) covalent geometry : angle 0.62113 (28023) hydrogen bonds : bond 0.09742 ( 1103) hydrogen bonds : angle 4.53669 ( 2712) *********************** 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 281 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 71 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7953 (ttm-80) REVERT: D 59 MET cc_start: 0.8102 (tpt) cc_final: 0.7660 (tpt) REVERT: D 86 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8036 (mmt-90) REVERT: E 60 LEU cc_start: 0.8527 (mt) cc_final: 0.8224 (mt) REVERT: F 55 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8464 (mtm-85) REVERT: F 79 LYS cc_start: 0.8084 (mttp) cc_final: 0.7858 (mttp) REVERT: F 85 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30) REVERT: G 73 ASN cc_start: 0.7897 (t0) cc_final: 0.7286 (t0) REVERT: H 83 TYR cc_start: 0.8482 (m-10) cc_final: 0.8188 (m-10) REVERT: M 68 TYR cc_start: 0.8352 (p90) cc_final: 0.8068 (p90) REVERT: M 155 GLN cc_start: 0.7442 (tt0) cc_final: 0.7188 (tt0) REVERT: U 70 TYR cc_start: 0.8753 (t80) cc_final: 0.8436 (t80) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1896 time to fit residues: 73.5597 Evaluate side-chains 237 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 104 GLN E 68 GLN E 125 GLN F 25 ASN F 27 GLN G 24 GLN G 110 ASN M 110 HIS N 95 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.150427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105720 restraints weight = 26285.797| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.30 r_work: 0.3177 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19486 Z= 0.280 Angle : 0.629 6.428 28023 Z= 0.367 Chirality : 0.040 0.153 3154 Planarity : 0.005 0.056 2171 Dihedral : 30.140 179.317 5718 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.99 % Allowed : 6.17 % Favored : 91.84 % 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: 1.02 (0.23), residues: 1272 helix: 1.69 (0.21), residues: 592 sheet: 0.31 (0.34), residues: 226 loop : -0.42 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 56 TYR 0.024 0.002 TYR G 50 PHE 0.016 0.002 PHE C 25 TRP 0.015 0.002 TRP M 196 HIS 0.008 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00641 (19486) covalent geometry : angle 0.62862 (28023) hydrogen bonds : bond 0.04351 ( 1103) hydrogen bonds : angle 3.66896 ( 2712) *********************** 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 271 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.521 Fit side-chains REVERT: B 26 ILE cc_start: 0.8715 (tp) cc_final: 0.8447 (tp) REVERT: C 64 GLU cc_start: 0.8213 (tt0) cc_final: 0.7980 (tt0) REVERT: C 71 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8264 (ttp-110) REVERT: D 59 MET cc_start: 0.8818 (tpt) cc_final: 0.8302 (tpt) REVERT: D 72 ARG cc_start: 0.8752 (mtp180) cc_final: 0.8522 (mtm180) REVERT: F 55 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8628 (mtm-85) REVERT: G 73 ASN cc_start: 0.8080 (t0) cc_final: 0.7485 (t0) REVERT: M 68 TYR cc_start: 0.8848 (p90) cc_final: 0.8624 (p90) REVERT: M 155 GLN cc_start: 0.8048 (tt0) cc_final: 0.7701 (tt0) outliers start: 22 outliers final: 17 residues processed: 257 average time/residue: 0.1858 time to fit residues: 66.1746 Evaluate side-chains 249 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 158 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 68 GLN E 125 GLN F 75 HIS U 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108921 restraints weight = 26432.373| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.32 r_work: 0.3228 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19486 Z= 0.167 Angle : 0.551 5.525 28023 Z= 0.328 Chirality : 0.035 0.144 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.902 179.118 5718 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.54 % Allowed : 10.24 % Favored : 88.21 % 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: 1.32 (0.23), residues: 1272 helix: 2.10 (0.21), residues: 592 sheet: 0.40 (0.35), residues: 214 loop : -0.46 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.014 0.001 TYR U 70 PHE 0.008 0.001 PHE G 25 TRP 0.008 0.001 TRP M 196 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (19486) covalent geometry : angle 0.55080 (28023) hydrogen bonds : bond 0.03466 ( 1103) hydrogen bonds : angle 3.30464 ( 2712) *********************** 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 261 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.602 Fit side-chains REVERT: B 26 ILE cc_start: 0.8368 (tp) cc_final: 0.8053 (tp) REVERT: C 64 GLU cc_start: 0.8089 (tt0) cc_final: 0.7853 (tt0) REVERT: G 73 ASN cc_start: 0.8021 (t0) cc_final: 0.7459 (t0) REVERT: H 83 TYR cc_start: 0.8844 (m-10) cc_final: 0.8459 (m-10) REVERT: H 89 ILE cc_start: 0.8596 (mt) cc_final: 0.8391 (mt) REVERT: N 98 GLU cc_start: 0.7941 (mp0) cc_final: 0.7410 (pm20) outliers start: 17 outliers final: 16 residues processed: 253 average time/residue: 0.1791 time to fit residues: 62.7337 Evaluate side-chains 247 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 104 GLN D 47 GLN E 68 GLN E 125 GLN M 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111917 restraints weight = 25803.596| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.43 r_work: 0.3301 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19486 Z= 0.221 Angle : 0.576 5.974 28023 Z= 0.339 Chirality : 0.037 0.156 3154 Planarity : 0.004 0.051 2171 Dihedral : 30.034 175.870 5718 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.54 % Allowed : 10.97 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.23), residues: 1272 helix: 2.10 (0.21), residues: 592 sheet: 0.24 (0.36), residues: 214 loop : -0.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 56 TYR 0.024 0.002 TYR U 90 PHE 0.011 0.001 PHE C 25 TRP 0.011 0.002 TRP N 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00502 (19486) covalent geometry : angle 0.57556 (28023) hydrogen bonds : bond 0.03830 ( 1103) hydrogen bonds : angle 3.34565 ( 2712) *********************** 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 268 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: B 26 ILE cc_start: 0.8465 (tp) cc_final: 0.8155 (tp) REVERT: C 15 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7874 (mtpp) REVERT: C 64 GLU cc_start: 0.8290 (tt0) cc_final: 0.8085 (tt0) REVERT: G 73 ASN cc_start: 0.8049 (t0) cc_final: 0.7474 (t0) REVERT: H 83 TYR cc_start: 0.8695 (m-10) cc_final: 0.8323 (m-10) REVERT: M 98 GLU cc_start: 0.6866 (mp0) cc_final: 0.6260 (pm20) REVERT: M 195 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: M 212 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8330 (mtpt) REVERT: N 89 ASP cc_start: 0.7309 (p0) cc_final: 0.7014 (m-30) REVERT: N 152 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8185 (mt0) REVERT: U 114 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7729 (ttpp) outliers start: 28 outliers final: 24 residues processed: 250 average time/residue: 0.1830 time to fit residues: 64.1040 Evaluate side-chains 252 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 47 GLN E 125 GLN N 110 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113826 restraints weight = 25693.335| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.44 r_work: 0.3323 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1826 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= 0.163 Angle : 0.553 6.884 28023 Z= 0.327 Chirality : 0.035 0.148 3154 Planarity : 0.004 0.050 2171 Dihedral : 29.953 175.923 5718 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.54 % Allowed : 11.70 % Favored : 85.77 % 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: 1.36 (0.23), residues: 1272 helix: 2.25 (0.21), residues: 592 sheet: 0.23 (0.35), residues: 214 loop : -0.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 56 TYR 0.026 0.002 TYR U 70 PHE 0.007 0.001 PHE C 25 TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00361 (19486) covalent geometry : angle 0.55337 (28023) hydrogen bonds : bond 0.03426 ( 1103) hydrogen bonds : angle 3.23161 ( 2712) *********************** 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 260 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.514 Fit side-chains REVERT: A 79 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8223 (ttpt) REVERT: B 26 ILE cc_start: 0.8372 (tp) cc_final: 0.8066 (tp) REVERT: C 15 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7766 (mtpp) REVERT: C 64 GLU cc_start: 0.8272 (tt0) cc_final: 0.8046 (tt0) REVERT: D 59 MET cc_start: 0.8480 (tpt) cc_final: 0.7919 (tpt) REVERT: G 73 ASN cc_start: 0.8041 (t0) cc_final: 0.7485 (t0) REVERT: H 33 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6733 (mtp-110) REVERT: H 83 TYR cc_start: 0.8705 (m-10) cc_final: 0.8379 (m-10) REVERT: M 98 GLU cc_start: 0.6958 (mp0) cc_final: 0.6354 (pm20) REVERT: M 195 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: N 152 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8165 (mt0) REVERT: N 216 LYS cc_start: 0.8432 (tppt) cc_final: 0.8151 (tptm) REVERT: U 83 ASN cc_start: 0.8208 (p0) cc_final: 0.7935 (p0) REVERT: U 114 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7743 (ttpp) outliers start: 28 outliers final: 22 residues processed: 245 average time/residue: 0.1897 time to fit residues: 64.9544 Evaluate side-chains 248 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.153995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112612 restraints weight = 25658.896| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.43 r_work: 0.3315 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19486 Z= 0.208 Angle : 0.567 6.568 28023 Z= 0.334 Chirality : 0.036 0.154 3154 Planarity : 0.004 0.050 2171 Dihedral : 29.952 174.692 5718 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.72 % Allowed : 12.60 % Favored : 84.68 % 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: 1.29 (0.23), residues: 1272 helix: 2.21 (0.21), residues: 592 sheet: 0.16 (0.36), residues: 214 loop : -0.56 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 56 TYR 0.015 0.002 TYR M 199 PHE 0.010 0.001 PHE G 25 TRP 0.010 0.001 TRP N 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00469 (19486) covalent geometry : angle 0.56695 (28023) hydrogen bonds : bond 0.03671 ( 1103) hydrogen bonds : angle 3.26048 ( 2712) *********************** 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 264 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8321 (ttpt) REVERT: A 133 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 26 ILE cc_start: 0.8348 (tp) cc_final: 0.8066 (tp) REVERT: C 15 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7838 (mtpp) REVERT: G 40 SER cc_start: 0.8632 (p) cc_final: 0.8364 (p) REVERT: G 73 ASN cc_start: 0.8070 (t0) cc_final: 0.7525 (t0) REVERT: H 33 ARG cc_start: 0.7191 (mmt90) cc_final: 0.6667 (mtp-110) REVERT: M 98 GLU cc_start: 0.6935 (mp0) cc_final: 0.6223 (pm20) REVERT: N 36 GLU cc_start: 0.7131 (pm20) cc_final: 0.6855 (pm20) REVERT: N 89 ASP cc_start: 0.7296 (p0) cc_final: 0.7022 (m-30) REVERT: N 152 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8031 (mt0) REVERT: N 216 LYS cc_start: 0.8517 (tppt) cc_final: 0.8206 (tptm) REVERT: U 114 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7859 (ttpp) outliers start: 30 outliers final: 26 residues processed: 248 average time/residue: 0.1780 time to fit residues: 62.0433 Evaluate side-chains 257 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN E 125 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113873 restraints weight = 25765.370| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.40 r_work: 0.3346 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2018 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= 0.162 Angle : 0.555 7.431 28023 Z= 0.327 Chirality : 0.035 0.148 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.917 175.063 5718 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.54 % Allowed : 13.24 % Favored : 84.22 % 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: 1.42 (0.23), residues: 1272 helix: 2.35 (0.21), residues: 592 sheet: 0.18 (0.35), residues: 214 loop : -0.52 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 56 TYR 0.023 0.001 TYR U 70 PHE 0.006 0.001 PHE C 25 TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00359 (19486) covalent geometry : angle 0.55505 (28023) hydrogen bonds : bond 0.03406 ( 1103) hydrogen bonds : angle 3.22109 ( 2712) *********************** 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 264 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.487 Fit side-chains REVERT: A 79 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8355 (ttpt) REVERT: B 26 ILE cc_start: 0.8236 (tp) cc_final: 0.7956 (tp) REVERT: C 15 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7748 (mtpp) REVERT: D 59 MET cc_start: 0.8478 (tpt) cc_final: 0.7928 (tpt) REVERT: G 40 SER cc_start: 0.8668 (p) cc_final: 0.8390 (p) REVERT: G 73 ASN cc_start: 0.8064 (t0) cc_final: 0.7514 (t0) REVERT: H 33 ARG cc_start: 0.7108 (mmt90) cc_final: 0.6603 (mtp-110) REVERT: M 98 GLU cc_start: 0.6937 (mp0) cc_final: 0.6257 (pm20) REVERT: N 89 ASP cc_start: 0.7237 (p0) cc_final: 0.6938 (m-30) REVERT: N 98 GLU cc_start: 0.7855 (mp0) cc_final: 0.7527 (pm20) REVERT: N 152 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8030 (mt0) REVERT: N 216 LYS cc_start: 0.8495 (tppt) cc_final: 0.8194 (tptm) REVERT: U 83 ASN cc_start: 0.8288 (p0) cc_final: 0.8065 (p0) REVERT: U 114 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7865 (ttpp) outliers start: 28 outliers final: 23 residues processed: 249 average time/residue: 0.1839 time to fit residues: 64.0658 Evaluate side-chains 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN C 104 GLN D 47 GLN E 125 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.153983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110712 restraints weight = 25828.485| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.41 r_work: 0.3309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19486 Z= 0.211 Angle : 0.571 6.747 28023 Z= 0.335 Chirality : 0.036 0.155 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.949 173.984 5718 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.81 % Allowed : 12.87 % Favored : 84.32 % 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: 1.29 (0.23), residues: 1272 helix: 2.26 (0.21), residues: 592 sheet: 0.08 (0.35), residues: 214 loop : -0.58 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.022 0.002 TYR U 90 PHE 0.010 0.001 PHE G 25 TRP 0.010 0.001 TRP N 185 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00476 (19486) covalent geometry : angle 0.57126 (28023) hydrogen bonds : bond 0.03715 ( 1103) hydrogen bonds : angle 3.28864 ( 2712) *********************** 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 261 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.328 Fit side-chains REVERT: B 26 ILE cc_start: 0.8298 (tp) cc_final: 0.8002 (tp) REVERT: C 15 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7840 (mtpp) REVERT: G 40 SER cc_start: 0.8752 (p) cc_final: 0.8480 (p) REVERT: G 73 ASN cc_start: 0.8100 (t0) cc_final: 0.7544 (t0) REVERT: H 33 ARG cc_start: 0.6912 (mmt90) cc_final: 0.6490 (mtp-110) REVERT: M 30 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: M 98 GLU cc_start: 0.6952 (mp0) cc_final: 0.6256 (pm20) REVERT: N 89 ASP cc_start: 0.7300 (p0) cc_final: 0.7009 (m-30) REVERT: N 152 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8067 (mt0) REVERT: N 216 LYS cc_start: 0.8466 (tppt) cc_final: 0.8155 (tptm) REVERT: U 114 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7932 (ttpp) outliers start: 31 outliers final: 27 residues processed: 244 average time/residue: 0.1824 time to fit residues: 61.8541 Evaluate side-chains 253 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 107 THR 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: 0.6980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN C 104 GLN E 125 GLN N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113664 restraints weight = 25677.977| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.43 r_work: 0.3338 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2161 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= 0.155 Angle : 0.557 9.650 28023 Z= 0.328 Chirality : 0.035 0.150 3154 Planarity : 0.004 0.048 2171 Dihedral : 29.931 173.959 5718 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.63 % Allowed : 13.24 % Favored : 84.13 % 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: 1.42 (0.23), residues: 1272 helix: 2.39 (0.21), residues: 592 sheet: 0.15 (0.36), residues: 204 loop : -0.55 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.021 0.001 TYR U 70 PHE 0.007 0.001 PHE G 25 TRP 0.007 0.001 TRP M 185 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00342 (19486) covalent geometry : angle 0.55689 (28023) hydrogen bonds : bond 0.03433 ( 1103) hydrogen bonds : angle 3.22679 ( 2712) *********************** 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 256 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.399 Fit side-chains REVERT: B 26 ILE cc_start: 0.8226 (tp) cc_final: 0.7928 (tp) REVERT: C 15 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7741 (mtpp) REVERT: D 59 MET cc_start: 0.8459 (tpt) cc_final: 0.7929 (tpt) REVERT: G 40 SER cc_start: 0.8732 (p) cc_final: 0.8455 (p) REVERT: G 73 ASN cc_start: 0.8093 (t0) cc_final: 0.7539 (t0) REVERT: H 33 ARG cc_start: 0.6825 (mmt90) cc_final: 0.6444 (mtp-110) REVERT: M 30 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7149 (mtm) REVERT: M 98 GLU cc_start: 0.6930 (mp0) cc_final: 0.6282 (pm20) REVERT: N 89 ASP cc_start: 0.7242 (p0) cc_final: 0.6964 (m-30) REVERT: N 152 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8043 (mt0) REVERT: N 216 LYS cc_start: 0.8411 (tppt) cc_final: 0.8117 (tptm) REVERT: U 80 ASP cc_start: 0.7932 (t0) cc_final: 0.7586 (t0) REVERT: U 83 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7946 (p0) REVERT: U 114 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7902 (ttpp) outliers start: 29 outliers final: 24 residues processed: 242 average time/residue: 0.1780 time to fit residues: 59.9182 Evaluate side-chains 247 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 83 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 137 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN E 125 GLN N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113861 restraints weight = 25653.802| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.48 r_work: 0.3339 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19486 Z= 0.154 Angle : 0.558 9.416 28023 Z= 0.328 Chirality : 0.034 0.146 3154 Planarity : 0.004 0.048 2171 Dihedral : 29.878 174.235 5718 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.27 % Allowed : 13.69 % Favored : 84.04 % 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: 1.50 (0.23), residues: 1272 helix: 2.45 (0.21), residues: 592 sheet: 0.20 (0.36), residues: 204 loop : -0.51 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 37 TYR 0.022 0.001 TYR U 90 PHE 0.008 0.001 PHE G 25 TRP 0.006 0.001 TRP N 54 HIS 0.003 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00342 (19486) covalent geometry : angle 0.55784 (28023) hydrogen bonds : bond 0.03326 ( 1103) hydrogen bonds : angle 3.18267 ( 2712) ********************** 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 247 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.506 Fit side-chains REVERT: B 26 ILE cc_start: 0.8211 (tp) cc_final: 0.7917 (tp) REVERT: C 15 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7733 (mtpp) REVERT: D 59 MET cc_start: 0.8456 (tpt) cc_final: 0.7944 (tpt) REVERT: G 40 SER cc_start: 0.8746 (p) cc_final: 0.8460 (p) REVERT: G 73 ASN cc_start: 0.8067 (t0) cc_final: 0.7542 (t0) REVERT: H 33 ARG cc_start: 0.6830 (mmt90) cc_final: 0.6450 (mtp-110) REVERT: M 98 GLU cc_start: 0.6907 (mp0) cc_final: 0.6292 (pm20) REVERT: N 89 ASP cc_start: 0.7259 (p0) cc_final: 0.6984 (m-30) REVERT: N 152 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8036 (mt0) REVERT: N 216 LYS cc_start: 0.8484 (tppt) cc_final: 0.8180 (tptm) REVERT: U 83 ASN cc_start: 0.8334 (p0) cc_final: 0.8126 (p0) REVERT: U 114 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7895 (ttpp) outliers start: 25 outliers final: 23 residues processed: 237 average time/residue: 0.1783 time to fit residues: 58.7603 Evaluate side-chains 244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain M residue 99 SER Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 162 GLU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 191 ARG Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 127 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN E 125 GLN N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112544 restraints weight = 25750.161| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.41 r_work: 0.3327 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19486 Z= 0.166 Angle : 0.548 9.526 28023 Z= 0.323 Chirality : 0.035 0.148 3154 Planarity : 0.004 0.049 2171 Dihedral : 29.787 174.241 5718 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.36 % Allowed : 13.96 % Favored : 83.68 % 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: 1.53 (0.23), residues: 1272 helix: 2.47 (0.21), residues: 592 sheet: 0.24 (0.36), residues: 204 loop : -0.51 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.018 0.001 TYR U 70 PHE 0.008 0.001 PHE G 25 TRP 0.008 0.001 TRP N 185 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00370 (19486) covalent geometry : angle 0.54791 (28023) hydrogen bonds : bond 0.03396 ( 1103) hydrogen bonds : angle 3.13394 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5674.66 seconds wall clock time: 97 minutes 28.77 seconds (5848.77 seconds total)