Starting phenix.real_space_refine on Thu Aug 6 12:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2026/8evg_28628.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 32 5.16 5 C 8886 2.51 5 N 2827 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15577 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 3.49, per 1000 atoms: 0.22 Number of scatterers: 15577 At special positions: 0 Unit cell: (138.336, 125.664, 124.608, 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 294 15.00 O 3538 8.00 N 2827 7.00 C 8886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 1.25 Conformation dependent library (CDL) restraints added in 527.1 milliseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 23 sheets defined 46.1% alpha, 18.2% beta 116 base pairs and 280 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 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 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.776A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.590A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.587A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.848A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.845A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.577A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.177A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.317A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR M 54 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR M 74 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE M 56 " --> pdb=" O TYR M 72 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR M 72 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP M 58 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.695A pdb=" N THR M 139 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.683A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 211 through 212 removed outlier: 6.531A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.676A pdb=" N GLY N 71 " --> pdb=" O TRP N 58 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.191A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 163 through 164 removed outlier: 3.624A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.531A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.439A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 280 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1968 1.31 - 1.43: 6054 1.43 - 1.56: 7989 1.56 - 1.69: 408 1.69 - 1.82: 55 Bond restraints: 16474 Sorted by residual: bond pdb=" O3' DG I 117 " pdb=" P DG I 118 " ideal model delta sigma weight residual 1.607 1.339 0.268 1.20e-02 6.94e+03 4.99e+02 bond pdb=" O3' DG J 80 " pdb=" P DG J 81 " ideal model delta sigma weight residual 1.607 1.359 0.248 1.20e-02 6.94e+03 4.26e+02 bond pdb=" O3' DG I 85 " pdb=" P DA I 86 " ideal model delta sigma weight residual 1.607 1.364 0.243 1.20e-02 6.94e+03 4.09e+02 bond pdb=" O3' DC I 107 " pdb=" P DA I 108 " ideal model delta sigma weight residual 1.607 1.370 0.237 1.20e-02 6.94e+03 3.89e+02 bond pdb=" O3' DT I 35 " pdb=" P DG I 36 " ideal model delta sigma weight residual 1.607 1.376 0.231 1.20e-02 6.94e+03 3.72e+02 ... (remaining 16469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 22929 5.87 - 11.74: 474 11.74 - 17.62: 95 17.62 - 23.49: 18 23.49 - 29.36: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" C3' DT J 34 " pdb=" O3' DT J 34 " pdb=" P DA J 35 " ideal model delta sigma weight residual 119.70 135.62 -15.92 1.20e+00 6.94e-01 1.76e+02 angle pdb=" C2' DG I 117 " pdb=" C1' DG I 117 " pdb=" N9 DG I 117 " ideal model delta sigma weight residual 114.30 95.96 18.34 1.40e+00 5.10e-01 1.72e+02 angle pdb=" O5' DC I 15 " pdb=" C5' DC I 15 " pdb=" C4' DC I 15 " ideal model delta sigma weight residual 109.40 118.43 -9.03 8.00e-01 1.56e+00 1.27e+02 angle pdb=" C3' DG I 127 " pdb=" O3' DG I 127 " pdb=" P DT I 128 " ideal model delta sigma weight residual 119.70 132.63 -12.93 1.20e+00 6.94e-01 1.16e+02 angle pdb=" C3' DT J 22 " pdb=" O3' DT J 22 " pdb=" P DG J 23 " ideal model delta sigma weight residual 119.70 132.38 -12.68 1.20e+00 6.94e-01 1.12e+02 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7209 32.94 - 65.88: 1834 65.88 - 98.82: 116 98.82 - 131.76: 2 131.76 - 164.70: 4 Dihedral angle restraints: 9165 sinusoidal: 5645 harmonic: 3520 Sorted by residual: dihedral pdb=" C4' DC I 20 " pdb=" C3' DC I 20 " pdb=" O3' DC I 20 " pdb=" P DT I 21 " ideal model delta sinusoidal sigma weight residual -140.00 24.70 -164.70 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " pdb=" P DT I 132 " ideal model delta sinusoidal sigma weight residual -140.00 24.49 -164.49 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 92 " pdb=" C3' DC I 92 " pdb=" O3' DC I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 62.35 157.65 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 2470 0.223 - 0.446: 139 0.446 - 0.670: 33 0.670 - 0.893: 8 0.893 - 1.116: 2 Chirality restraints: 2652 Sorted by residual: chirality pdb=" C3' DG I 53 " pdb=" C4' DG I 53 " pdb=" O3' DG I 53 " pdb=" C2' DG I 53 " both_signs ideal model delta sigma weight residual False -2.73 -1.61 -1.12 2.00e-01 2.50e+01 3.11e+01 chirality pdb=" C3' DC I 92 " pdb=" C4' DC I 92 " pdb=" O3' DC I 92 " pdb=" C2' DC I 92 " both_signs ideal model delta sigma weight residual False -2.73 -1.68 -1.05 2.00e-01 2.50e+01 2.76e+01 chirality pdb=" C3' DA J 97 " pdb=" C4' DA J 97 " pdb=" O3' DA J 97 " pdb=" C2' DA J 97 " both_signs ideal model delta sigma weight residual False -2.73 -1.89 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 2649 not shown) Planarity restraints: 1948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 68 " -0.119 2.00e-02 2.50e+03 6.09e-02 9.28e+01 pdb=" N1 DT J 68 " 0.098 2.00e-02 2.50e+03 pdb=" C2 DT J 68 " 0.007 2.00e-02 2.50e+03 pdb=" O2 DT J 68 " 0.064 2.00e-02 2.50e+03 pdb=" N3 DT J 68 " -0.079 2.00e-02 2.50e+03 pdb=" C4 DT J 68 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT J 68 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DT J 68 " 0.045 2.00e-02 2.50e+03 pdb=" C7 DT J 68 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT J 68 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 98 " 0.117 2.00e-02 2.50e+03 5.78e-02 9.19e+01 pdb=" N9 DA I 98 " -0.123 2.00e-02 2.50e+03 pdb=" C8 DA I 98 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA I 98 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 98 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA I 98 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 98 " 0.024 2.00e-02 2.50e+03 pdb=" N1 DA I 98 " 0.061 2.00e-02 2.50e+03 pdb=" C2 DA I 98 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DA I 98 " -0.040 2.00e-02 2.50e+03 pdb=" C4 DA I 98 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 122 " 0.098 2.00e-02 2.50e+03 5.04e-02 7.61e+01 pdb=" N9 DG J 122 " -0.063 2.00e-02 2.50e+03 pdb=" C8 DG J 122 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" C5 DG J 122 " 0.034 2.00e-02 2.50e+03 pdb=" C6 DG J 122 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 122 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J 122 " 0.050 2.00e-02 2.50e+03 pdb=" C2 DG J 122 " 0.012 2.00e-02 2.50e+03 pdb=" N2 DG J 122 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG J 122 " -0.104 2.00e-02 2.50e+03 pdb=" C4 DG J 122 " -0.026 2.00e-02 2.50e+03 ... (remaining 1945 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 27 2.42 - 3.04: 8939 3.04 - 3.66: 23614 3.66 - 4.28: 41684 4.28 - 4.90: 62662 Nonbonded interactions: 136926 Sorted by model distance: nonbonded pdb=" N2 DG I 109 " pdb=" O2 DC J 54 " model vdw 1.794 3.120 nonbonded pdb=" N2 DG I 25 " pdb=" O2 DC J 138 " model vdw 1.815 2.496 nonbonded pdb=" O2 DC I 134 " pdb=" N2 DG J 29 " model vdw 2.066 2.496 nonbonded pdb=" OD2 ASP M 95 " pdb=" OG SER M 98 " model vdw 2.219 3.040 nonbonded pdb=" N2 DG I 53 " pdb=" O2 DT J 111 " model vdw 2.227 3.120 ... (remaining 136921 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' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.020 0.268 16478 Z= 1.534 Angle : 2.014 29.362 23529 Z= 1.183 Chirality : 0.126 1.116 2652 Planarity : 0.010 0.086 1948 Dihedral : 28.950 164.699 6897 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.29 % Allowed : 20.41 % Favored : 79.30 % 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: 1.12 (0.25), residues: 1188 helix: 2.19 (0.22), residues: 543 sheet: -0.04 (0.35), residues: 226 loop : -0.74 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 219 TYR 0.024 0.001 TYR H 37 PHE 0.013 0.001 PHE D 67 TRP 0.007 0.001 TRP N 69 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.01971 / 1.53 (16474) covalent geometry : angle 2.01438 / 1.18 (23521) SS BOND : bond 0.00321 / 0.16 ( 4) SS BOND : angle 1.37826 / 0.62 ( 8) hydrogen bonds : bond 0.21737 / 14.78 ( 796) hydrogen bonds : angle 9.61473 / 6.94 ( 2028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 288 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7908 (mtt) cc_final: 0.7702 (mtt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 0.8507 time to fit residues: 263.7475 Evaluate side-chains 191 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 46 HIS E 39 HIS E 108 ASN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN N 25 GLN N 196 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.106480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070248 restraints weight = 30355.550| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.05 r_work: 0.2861 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16478 Z= 0.259 Angle : 0.979 13.618 23529 Z= 0.507 Chirality : 0.069 0.351 2652 Planarity : 0.005 0.049 1948 Dihedral : 31.361 178.647 4574 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.89 % Allowed : 22.45 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1188 helix: 2.38 (0.22), residues: 544 sheet: 0.22 (0.35), residues: 226 loop : -0.86 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 219 TYR 0.015 0.002 TYR N 76 PHE 0.011 0.001 PHE E 67 TRP 0.012 0.002 TRP M 132 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 (16474) covalent geometry : angle 0.97823 / 0.51 (23521) SS BOND : bond 0.00391 / 0.20 ( 4) SS BOND : angle 1.75704 / 0.81 ( 8) hydrogen bonds : bond 0.06615 / 4.59 ( 796) hydrogen bonds : angle 3.74583 / 2.67 ( 2028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8848 (mtpt) cc_final: 0.8574 (mttp) REVERT: C 91 GLU cc_start: 0.8713 (tp30) cc_final: 0.8480 (tp30) REVERT: D 39 TYR cc_start: 0.8479 (t80) cc_final: 0.7686 (t80) REVERT: D 113 LYS cc_start: 0.9220 (ttpt) cc_final: 0.8959 (ttpt) REVERT: E 120 MET cc_start: 0.8955 (mtt) cc_final: 0.8748 (mtt) REVERT: F 44 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8429 (mttp) REVERT: G 90 ASP cc_start: 0.8977 (t0) cc_final: 0.8726 (t0) REVERT: M 251 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8319 (mm-30) REVERT: N 95 ASP cc_start: 0.8218 (t0) cc_final: 0.7970 (t0) REVERT: N 161 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8706 (tptp) REVERT: N 173 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8581 (tm) REVERT: N 237 GLU cc_start: 0.6328 (mp0) cc_final: 0.5714 (mp0) outliers start: 40 outliers final: 11 residues processed: 236 average time/residue: 0.7270 time to fit residues: 185.5041 Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 138 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 108 ASN D 46 HIS E 39 HIS E 55 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070340 restraints weight = 30451.391| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.07 r_work: 0.2863 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16478 Z= 0.162 Angle : 0.752 9.977 23529 Z= 0.413 Chirality : 0.053 0.304 2652 Planarity : 0.005 0.037 1948 Dihedral : 30.785 178.889 4573 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.92 % Allowed : 23.32 % Favored : 73.76 % 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: 1.46 (0.25), residues: 1188 helix: 2.60 (0.22), residues: 544 sheet: 0.30 (0.35), residues: 226 loop : -0.88 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.012 0.001 TYR N 117 PHE 0.010 0.001 PHE A 67 TRP 0.009 0.001 TRP N 58 HIS 0.008 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (16474) covalent geometry : angle 0.75223 / 0.41 (23521) SS BOND : bond 0.00289 / 0.14 ( 4) SS BOND : angle 1.18337 / 0.53 ( 8) hydrogen bonds : bond 0.05041 / 3.51 ( 796) hydrogen bonds : angle 3.44658 / 2.46 ( 2028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8852 (mp) cc_final: 0.8591 (mt) REVERT: B 44 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8537 (mttp) REVERT: C 91 GLU cc_start: 0.8776 (tp30) cc_final: 0.8516 (tp30) REVERT: D 39 TYR cc_start: 0.8474 (t80) cc_final: 0.7662 (t80) REVERT: D 76 ARG cc_start: 0.8422 (mtm180) cc_final: 0.8141 (mtm-85) REVERT: D 113 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8966 (ttpt) REVERT: G 90 ASP cc_start: 0.8943 (t0) cc_final: 0.8583 (t0) REVERT: H 56 MET cc_start: 0.9336 (tpp) cc_final: 0.9076 (tpp) REVERT: M 95 ASP cc_start: 0.7475 (t70) cc_final: 0.7234 (t0) REVERT: N 95 ASP cc_start: 0.8415 (t0) cc_final: 0.8083 (t0) REVERT: N 161 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8751 (tptp) REVERT: N 173 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (tm) REVERT: N 237 GLU cc_start: 0.6713 (mp0) cc_final: 0.6108 (mp0) REVERT: N 240 ASP cc_start: 0.8439 (m-30) cc_final: 0.8120 (m-30) outliers start: 30 outliers final: 9 residues processed: 216 average time/residue: 0.7764 time to fit residues: 181.2936 Evaluate side-chains 196 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 172 SER Chi-restraints excluded: chain M residue 175 GLU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 134 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN D 46 HIS E 39 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071196 restraints weight = 30450.578| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.00 r_work: 0.2887 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16478 Z= 0.128 Angle : 0.675 9.268 23529 Z= 0.374 Chirality : 0.049 0.318 2652 Planarity : 0.004 0.044 1948 Dihedral : 30.607 179.240 4573 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 24.30 % Favored : 72.98 % 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: 1.65 (0.25), residues: 1188 helix: 2.76 (0.22), residues: 544 sheet: 0.47 (0.36), residues: 226 loop : -0.85 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.009 0.001 TYR N 117 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.001 TRP N 199 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (16474) covalent geometry : angle 0.67441 / 0.37 (23521) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 1.03555 / 0.47 ( 8) hydrogen bonds : bond 0.04520 / 3.20 ( 796) hydrogen bonds : angle 3.28765 / 2.34 ( 2028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8856 (mp) cc_final: 0.8614 (mt) REVERT: B 79 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8794 (mttm) REVERT: D 39 TYR cc_start: 0.8505 (t80) cc_final: 0.7679 (t80) REVERT: D 76 ARG cc_start: 0.8452 (mtm180) cc_final: 0.8214 (mtm-85) REVERT: D 113 LYS cc_start: 0.9229 (ttpt) cc_final: 0.8971 (ttpt) REVERT: E 39 HIS cc_start: 0.6800 (t70) cc_final: 0.6533 (t70) REVERT: E 90 MET cc_start: 0.8791 (tpp) cc_final: 0.8499 (mmm) REVERT: G 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8508 (t0) REVERT: H 60 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8763 (m110) REVERT: M 95 ASP cc_start: 0.7569 (t70) cc_final: 0.7313 (t0) REVERT: N 95 ASP cc_start: 0.8478 (t70) cc_final: 0.8189 (t70) REVERT: N 237 GLU cc_start: 0.6939 (mp0) cc_final: 0.6299 (mp0) REVERT: N 240 ASP cc_start: 0.8438 (m-30) cc_final: 0.8158 (m-30) outliers start: 28 outliers final: 9 residues processed: 210 average time/residue: 0.7683 time to fit residues: 174.5643 Evaluate side-chains 194 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 129 optimal weight: 0.1980 chunk 134 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 100 optimal weight: 0.0770 chunk 102 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 108 ASN D 46 HIS E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN M 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071764 restraints weight = 31009.582| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.10 r_work: 0.2967 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16478 Z= 0.121 Angle : 0.650 9.905 23529 Z= 0.362 Chirality : 0.047 0.268 2652 Planarity : 0.004 0.039 1948 Dihedral : 30.391 178.557 4573 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.94 % Allowed : 26.53 % Favored : 71.53 % 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: 1.78 (0.25), residues: 1188 helix: 2.84 (0.22), residues: 545 sheet: 0.57 (0.37), residues: 226 loop : -0.78 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.015 0.001 TYR E 54 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.001 TRP N 199 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (16474) covalent geometry : angle 0.64994 / 0.36 (23521) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 0.97161 / 0.44 ( 8) hydrogen bonds : bond 0.04269 / 3.02 ( 796) hydrogen bonds : angle 3.21081 / 2.29 ( 2028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8664 (mp) cc_final: 0.8460 (mt) REVERT: B 79 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8586 (mttm) REVERT: D 39 TYR cc_start: 0.8230 (t80) cc_final: 0.7380 (t80) REVERT: D 76 ARG cc_start: 0.8310 (mtm180) cc_final: 0.8029 (mtm-85) REVERT: D 113 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8746 (ttpt) REVERT: E 39 HIS cc_start: 0.6637 (t70) cc_final: 0.6348 (t70) REVERT: E 90 MET cc_start: 0.8678 (tpp) cc_final: 0.8271 (mmm) REVERT: F 44 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8354 (mttm) REVERT: G 90 ASP cc_start: 0.8785 (t0) cc_final: 0.8290 (t0) REVERT: H 56 MET cc_start: 0.9275 (tpp) cc_final: 0.8877 (tpp) REVERT: H 60 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8545 (m110) REVERT: M 95 ASP cc_start: 0.7390 (t70) cc_final: 0.7063 (t0) REVERT: N 84 GLU cc_start: 0.8068 (tp30) cc_final: 0.7631 (mp0) REVERT: N 95 ASP cc_start: 0.8275 (t70) cc_final: 0.7845 (t70) REVERT: N 237 GLU cc_start: 0.6906 (mp0) cc_final: 0.6366 (mp0) outliers start: 20 outliers final: 7 residues processed: 200 average time/residue: 0.7660 time to fit residues: 165.5034 Evaluate side-chains 191 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 50.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN D 46 HIS D 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 ASN N 196 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.066596 restraints weight = 30646.090| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.05 r_work: 0.2857 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16478 Z= 0.240 Angle : 0.723 9.858 23529 Z= 0.390 Chirality : 0.050 0.288 2652 Planarity : 0.005 0.038 1948 Dihedral : 30.609 179.480 4573 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.72 % Allowed : 25.46 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1188 helix: 2.56 (0.22), residues: 543 sheet: 0.57 (0.37), residues: 226 loop : -0.92 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.020 0.002 TYR E 54 PHE 0.013 0.002 PHE E 67 TRP 0.022 0.002 TRP N 58 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.24 (16474) covalent geometry : angle 0.72229 / 0.39 (23521) SS BOND : bond 0.00674 / 0.34 ( 4) SS BOND : angle 1.83151 / 0.84 ( 8) hydrogen bonds : bond 0.05534 / 3.84 ( 796) hydrogen bonds : angle 3.43887 / 2.45 ( 2028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8667 (mp) cc_final: 0.8460 (mt) REVERT: C 56 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8596 (tt0) REVERT: D 39 TYR cc_start: 0.8376 (t80) cc_final: 0.7492 (t80) REVERT: D 68 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7995 (mt-10) REVERT: E 90 MET cc_start: 0.8817 (tpp) cc_final: 0.8519 (tpp) REVERT: G 90 ASP cc_start: 0.8805 (t0) cc_final: 0.8399 (t0) REVERT: H 60 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: M 95 ASP cc_start: 0.7709 (t70) cc_final: 0.7383 (t0) REVERT: M 176 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8338 (ttm110) REVERT: M 234 ASN cc_start: 0.7534 (p0) cc_final: 0.6975 (m-40) REVERT: N 84 GLU cc_start: 0.8234 (tp30) cc_final: 0.7907 (mp0) REVERT: N 95 ASP cc_start: 0.8472 (t70) cc_final: 0.7984 (t70) REVERT: N 111 GLU cc_start: 0.9153 (pt0) cc_final: 0.8841 (pp20) REVERT: N 161 LYS cc_start: 0.9329 (ttpp) cc_final: 0.9057 (tptp) REVERT: N 162 MET cc_start: 0.8506 (mmm) cc_final: 0.7913 (mmm) outliers start: 28 outliers final: 14 residues processed: 206 average time/residue: 0.7366 time to fit residues: 164.4758 Evaluate side-chains 201 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 110 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN N 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069978 restraints weight = 30769.419| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.05 r_work: 0.2921 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16478 Z= 0.125 Angle : 0.635 9.094 23529 Z= 0.354 Chirality : 0.045 0.265 2652 Planarity : 0.004 0.041 1948 Dihedral : 30.308 178.276 4573 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 27.02 % Favored : 71.14 % 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: 1.71 (0.25), residues: 1188 helix: 2.80 (0.22), residues: 542 sheet: 0.55 (0.37), residues: 226 loop : -0.81 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 71 TYR 0.019 0.001 TYR E 54 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 132 HIS 0.005 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (16474) covalent geometry : angle 0.63468 / 0.35 (23521) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 0.79284 / 0.35 ( 8) hydrogen bonds : bond 0.04335 / 3.07 ( 796) hydrogen bonds : angle 3.26221 / 2.32 ( 2028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8549 (pt0) cc_final: 0.8062 (pm20) REVERT: B 79 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (mttm) REVERT: C 56 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: D 39 TYR cc_start: 0.8209 (t80) cc_final: 0.7329 (t80) REVERT: D 68 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7975 (mt-10) REVERT: D 76 ARG cc_start: 0.8227 (mtm180) cc_final: 0.8012 (mtm-85) REVERT: E 39 HIS cc_start: 0.6753 (t70) cc_final: 0.6403 (t70) REVERT: E 56 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8738 (ttpp) REVERT: E 90 MET cc_start: 0.8716 (tpp) cc_final: 0.8289 (mmm) REVERT: G 90 ASP cc_start: 0.8721 (t0) cc_final: 0.8234 (t0) REVERT: H 60 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8614 (m110) REVERT: M 95 ASP cc_start: 0.7721 (t70) cc_final: 0.7395 (t0) REVERT: M 234 ASN cc_start: 0.7478 (p0) cc_final: 0.6873 (m-40) REVERT: N 95 ASP cc_start: 0.8457 (t70) cc_final: 0.8021 (t70) REVERT: N 111 GLU cc_start: 0.9101 (pt0) cc_final: 0.8793 (pp20) REVERT: N 161 LYS cc_start: 0.9281 (ttpp) cc_final: 0.8991 (tptp) REVERT: N 162 MET cc_start: 0.8279 (mmm) cc_final: 0.7841 (mmm) REVERT: N 240 ASP cc_start: 0.8843 (m-30) cc_final: 0.8336 (m-30) outliers start: 19 outliers final: 8 residues processed: 205 average time/residue: 0.6984 time to fit residues: 155.2412 Evaluate side-chains 195 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN N 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067419 restraints weight = 30750.627| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.04 r_work: 0.2872 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16478 Z= 0.189 Angle : 0.674 12.313 23529 Z= 0.368 Chirality : 0.046 0.274 2652 Planarity : 0.004 0.038 1948 Dihedral : 30.321 179.423 4573 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.85 % Allowed : 27.60 % Favored : 70.55 % 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: 1.56 (0.25), residues: 1188 helix: 2.64 (0.22), residues: 543 sheet: 0.53 (0.36), residues: 226 loop : -0.88 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 176 TYR 0.017 0.001 TYR E 54 PHE 0.010 0.001 PHE E 67 TRP 0.011 0.002 TRP N 58 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (16474) covalent geometry : angle 0.67371 / 0.37 (23521) SS BOND : bond 0.00478 / 0.24 ( 4) SS BOND : angle 1.79860 / 0.85 ( 8) hydrogen bonds : bond 0.04835 / 3.39 ( 796) hydrogen bonds : angle 3.34985 / 2.40 ( 2028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: C 90 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8677 (t70) REVERT: D 68 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8019 (mt-10) REVERT: E 39 HIS cc_start: 0.6749 (t70) cc_final: 0.6408 (t70) REVERT: E 90 MET cc_start: 0.8767 (tpp) cc_final: 0.8470 (tpp) REVERT: G 90 ASP cc_start: 0.8667 (t0) cc_final: 0.8204 (t0) REVERT: H 56 MET cc_start: 0.9266 (tpp) cc_final: 0.8846 (tpp) REVERT: H 60 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8751 (m-40) REVERT: M 95 ASP cc_start: 0.7825 (t70) cc_final: 0.7584 (OUTLIER) REVERT: M 176 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8019 (ttm110) REVERT: M 234 ASN cc_start: 0.7808 (p0) cc_final: 0.7014 (m-40) REVERT: N 84 GLU cc_start: 0.8278 (tp30) cc_final: 0.8069 (mp0) REVERT: N 95 ASP cc_start: 0.8494 (t70) cc_final: 0.8073 (t70) REVERT: N 111 GLU cc_start: 0.9178 (pt0) cc_final: 0.8849 (pp20) REVERT: N 161 LYS cc_start: 0.9307 (ttpp) cc_final: 0.9020 (tptp) REVERT: N 162 MET cc_start: 0.8429 (mmm) cc_final: 0.7791 (mmm) outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 0.7448 time to fit residues: 163.6184 Evaluate side-chains 198 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 20.0000 chunk 126 optimal weight: 0.0970 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 0.4980 chunk 89 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067968 restraints weight = 30715.434| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.03 r_work: 0.2896 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16478 Z= 0.160 Angle : 0.649 10.652 23529 Z= 0.358 Chirality : 0.045 0.272 2652 Planarity : 0.004 0.041 1948 Dihedral : 30.238 179.633 4573 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 28.67 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1188 helix: 2.67 (0.22), residues: 543 sheet: 0.50 (0.36), residues: 226 loop : -0.85 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 176 TYR 0.039 0.001 TYR N 76 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP N 132 HIS 0.005 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (16474) covalent geometry : angle 0.64904 / 0.36 (23521) SS BOND : bond 0.00409 / 0.21 ( 4) SS BOND : angle 0.98712 / 0.43 ( 8) hydrogen bonds : bond 0.04388 / 3.10 ( 796) hydrogen bonds : angle 3.31831 / 2.37 ( 2028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8569 (pt0) cc_final: 0.8125 (pm20) REVERT: B 22 LEU cc_start: 0.8488 (mt) cc_final: 0.8114 (mp) REVERT: C 56 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: D 39 TYR cc_start: 0.8248 (t80) cc_final: 0.7380 (t80) REVERT: D 68 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8067 (mt-10) REVERT: E 39 HIS cc_start: 0.6821 (t70) cc_final: 0.6474 (t70) REVERT: E 56 LYS cc_start: 0.9139 (ttpp) cc_final: 0.8829 (ttpp) REVERT: E 90 MET cc_start: 0.8792 (tpp) cc_final: 0.8505 (tpp) REVERT: G 90 ASP cc_start: 0.8646 (t0) cc_final: 0.8171 (t0) REVERT: H 60 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8668 (m110) REVERT: M 95 ASP cc_start: 0.7822 (t70) cc_final: 0.7609 (OUTLIER) REVERT: M 112 ASP cc_start: 0.8245 (t0) cc_final: 0.7479 (m-30) REVERT: M 176 ARG cc_start: 0.8487 (ttm110) cc_final: 0.7920 (ttm110) REVERT: M 234 ASN cc_start: 0.7784 (p0) cc_final: 0.6969 (m-40) REVERT: N 84 GLU cc_start: 0.8151 (tp30) cc_final: 0.7823 (mp0) REVERT: N 95 ASP cc_start: 0.8547 (t70) cc_final: 0.8141 (t70) REVERT: N 111 GLU cc_start: 0.9157 (pt0) cc_final: 0.8852 (pp20) REVERT: N 161 LYS cc_start: 0.9299 (ttpp) cc_final: 0.9009 (tptp) REVERT: N 162 MET cc_start: 0.8355 (mmm) cc_final: 0.7835 (mmm) outliers start: 12 outliers final: 10 residues processed: 195 average time/residue: 0.7288 time to fit residues: 153.7844 Evaluate side-chains 195 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 50.0000 chunk 68 optimal weight: 0.4980 chunk 118 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.106168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069248 restraints weight = 30789.855| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.03 r_work: 0.2906 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16478 Z= 0.134 Angle : 0.636 9.043 23529 Z= 0.354 Chirality : 0.044 0.272 2652 Planarity : 0.004 0.043 1948 Dihedral : 30.145 179.607 4573 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.26 % Allowed : 28.67 % Favored : 70.07 % 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: 1.63 (0.25), residues: 1188 helix: 2.71 (0.22), residues: 543 sheet: 0.51 (0.36), residues: 226 loop : -0.82 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 176 TYR 0.018 0.001 TYR E 54 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (16474) covalent geometry : angle 0.63625 / 0.35 (23521) SS BOND : bond 0.00308 / 0.16 ( 4) SS BOND : angle 0.82048 / 0.35 ( 8) hydrogen bonds : bond 0.04279 / 3.04 ( 796) hydrogen bonds : angle 3.29393 / 2.35 ( 2028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8544 (pt0) cc_final: 0.8045 (pm20) REVERT: C 13 LYS cc_start: 0.8743 (tppp) cc_final: 0.8429 (tptp) REVERT: C 56 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: D 39 TYR cc_start: 0.8133 (t80) cc_final: 0.7258 (t80) REVERT: D 68 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7964 (mt-10) REVERT: E 39 HIS cc_start: 0.6757 (t70) cc_final: 0.6430 (t70) REVERT: E 56 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8803 (ttpp) REVERT: E 90 MET cc_start: 0.8695 (tpp) cc_final: 0.8399 (tpp) REVERT: G 90 ASP cc_start: 0.8670 (t0) cc_final: 0.8161 (t0) REVERT: H 60 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8583 (m110) REVERT: M 95 ASP cc_start: 0.7737 (t70) cc_final: 0.7517 (OUTLIER) REVERT: M 112 ASP cc_start: 0.8219 (t0) cc_final: 0.7438 (m-30) REVERT: M 176 ARG cc_start: 0.8518 (ttm110) cc_final: 0.7926 (ttm110) REVERT: M 234 ASN cc_start: 0.7808 (p0) cc_final: 0.6900 (m-40) REVERT: N 32 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7455 (mm-30) REVERT: N 84 GLU cc_start: 0.8129 (tp30) cc_final: 0.7803 (mp0) REVERT: N 95 ASP cc_start: 0.8471 (t70) cc_final: 0.8046 (t70) REVERT: N 111 GLU cc_start: 0.9168 (pt0) cc_final: 0.8848 (pp20) REVERT: N 161 LYS cc_start: 0.9308 (ttpp) cc_final: 0.9005 (tptp) REVERT: N 162 MET cc_start: 0.8315 (mmm) cc_final: 0.7818 (mmm) outliers start: 13 outliers final: 9 residues processed: 197 average time/residue: 0.7451 time to fit residues: 158.6677 Evaluate side-chains 197 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 115 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 117 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068959 restraints weight = 30418.394| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.05 r_work: 0.2908 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16478 Z= 0.129 Angle : 0.632 11.013 23529 Z= 0.350 Chirality : 0.044 0.273 2652 Planarity : 0.004 0.041 1948 Dihedral : 30.063 179.645 4573 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 28.96 % Favored : 69.87 % 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: 1.65 (0.25), residues: 1188 helix: 2.72 (0.22), residues: 543 sheet: 0.50 (0.36), residues: 226 loop : -0.79 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 23 TYR 0.019 0.001 TYR E 54 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 132 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (16474) covalent geometry : angle 0.63236 / 0.35 (23521) SS BOND : bond 0.00280 / 0.14 ( 4) SS BOND : angle 0.79440 / 0.34 ( 8) hydrogen bonds : bond 0.04219 / 3.00 ( 796) hydrogen bonds : angle 3.26813 / 2.34 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5200.90 seconds wall clock time: 89 minutes 15.42 seconds (5355.42 seconds total)