Starting phenix.real_space_refine on Sat Aug 23 22:55:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evg_28628/08_2025/8evg_28628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evg_28628/08_2025/8evg_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_2025/8evg_28628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2025/8evg_28628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2025/8evg_28628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evg_28628/08_2025/8evg_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-2.0-5787/lib/python3.9/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: 3.76, per 1000 atoms: 0.24 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: 1.31 Conformation dependent library (CDL) restraints added in 510.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.73 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: 3.19 Time building geometry restraints manager: 1.79 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 1.50e-02 4.44e+03 3.19e+02 bond pdb=" O3' DG J 80 " pdb=" P DG J 81 " ideal model delta sigma weight residual 1.607 1.359 0.248 1.50e-02 4.44e+03 2.73e+02 bond pdb=" O3' DG I 85 " pdb=" P DA I 86 " ideal model delta sigma weight residual 1.607 1.364 0.243 1.50e-02 4.44e+03 2.62e+02 bond pdb=" O3' DC I 107 " pdb=" P DA I 108 " ideal model delta sigma weight residual 1.607 1.370 0.237 1.50e-02 4.44e+03 2.49e+02 bond pdb=" O3' DT I 35 " pdb=" P DG I 36 " ideal model delta sigma weight residual 1.607 1.376 0.231 1.50e-02 4.44e+03 2.38e+02 ... (remaining 16469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 22934 5.87 - 11.74: 464 11.74 - 17.62: 101 17.62 - 23.49: 17 23.49 - 29.36: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" O3' DC I 96 " pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 111.50 90.34 21.16 1.50e+00 4.44e-01 1.99e+02 angle pdb=" O3' DA J 82 " pdb=" C3' DA J 82 " pdb=" C2' DA J 82 " ideal model delta sigma weight residual 111.50 90.71 20.79 1.50e+00 4.44e-01 1.92e+02 angle pdb=" O3' DA J 97 " pdb=" C3' DA J 97 " pdb=" C2' DA J 97 " ideal model delta sigma weight residual 111.50 130.96 -19.46 1.50e+00 4.44e-01 1.68e+02 angle pdb=" C4' DT I 131 " pdb=" C3' DT I 131 " pdb=" O3' DT I 131 " ideal model delta sigma weight residual 110.00 129.08 -19.08 1.50e+00 4.44e-01 1.62e+02 angle pdb=" O3' DC J 19 " pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 111.50 130.56 -19.06 1.50e+00 4.44e-01 1.62e+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 - 0.209: 2394 0.209 - 0.418: 211 0.418 - 0.627: 34 0.627 - 0.836: 11 0.836 - 1.045: 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 -2.66 -1.61 -1.05 2.00e-01 2.50e+01 2.73e+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 -2.66 -1.68 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" P DT I 87 " pdb=" OP1 DT I 87 " pdb=" OP2 DT I 87 " pdb=" O5' DT I 87 " both_signs ideal model delta sigma weight residual True 2.35 -1.55 0.80 2.00e-01 2.50e+01 1.59e+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: 0.930 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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= 1.096 Angle : 2.029 29.362 23529 Z= 1.164 Chirality : 0.131 1.045 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 aren 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 covalent geometry : bond 0.02007 (16474) covalent geometry : angle 2.02965 (23521) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.37826 ( 8) hydrogen bonds : bond 0.21737 ( 796) hydrogen bonds : angle 9.61473 ( 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 : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7907 (mtt) cc_final: 0.7703 (mtt) outliers start: 3 outliers final: 1 residues processed: 289 average time/residue: 0.9194 time to fit residues: 283.7967 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 : 0.466 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN 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 N 235 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070403 restraints weight = 30592.361| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.10 r_work: 0.2934 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16478 Z= 0.211 Angle : 0.684 8.944 23529 Z= 0.396 Chirality : 0.041 0.208 2652 Planarity : 0.005 0.047 1948 Dihedral : 30.464 176.931 4574 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.30 % Allowed : 23.13 % Favored : 73.57 % 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 aren not related in a simple way. whole: 1.44 (0.25), residues: 1188 helix: 2.51 (0.22), residues: 544 sheet: 0.26 (0.35), residues: 226 loop : -0.77 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.011 0.001 TYR N 117 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.001 TRP M 132 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00480 (16474) covalent geometry : angle 0.68344 (23521) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.72806 ( 8) hydrogen bonds : bond 0.04895 ( 796) hydrogen bonds : angle 3.43913 ( 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 246 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7206 (t70) cc_final: 0.6919 (t-90) REVERT: B 44 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8332 (mttp) REVERT: C 90 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8604 (t70) REVERT: C 91 GLU cc_start: 0.8745 (tp30) cc_final: 0.8438 (tp30) REVERT: D 39 TYR cc_start: 0.8186 (t80) cc_final: 0.7401 (t80) REVERT: D 113 LYS cc_start: 0.8963 (ttpt) cc_final: 0.8636 (ttpt) REVERT: E 42 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7500 (mmm-85) REVERT: E 90 MET cc_start: 0.8685 (mmm) cc_final: 0.8387 (tpp) REVERT: G 90 ASP cc_start: 0.8946 (t0) cc_final: 0.8498 (t0) REVERT: M 45 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7804 (tmtm) REVERT: M 251 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8372 (mm-30) REVERT: N 95 ASP cc_start: 0.8174 (t0) cc_final: 0.7857 (t0) REVERT: N 161 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8815 (tptp) REVERT: N 173 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8441 (tm) REVERT: N 235 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (p0) outliers start: 34 outliers final: 7 residues processed: 233 average time/residue: 0.7634 time to fit residues: 191.5554 Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER Chi-restraints excluded: chain M residue 239 ASP Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 235 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069680 restraints weight = 30739.041| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.09 r_work: 0.2919 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16478 Z= 0.169 Angle : 0.600 8.713 23529 Z= 0.350 Chirality : 0.037 0.168 2652 Planarity : 0.004 0.036 1948 Dihedral : 30.133 178.962 4573 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.43 % Allowed : 24.00 % Favored : 73.57 % 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 aren not related in a simple way. whole: 1.59 (0.25), residues: 1188 helix: 2.66 (0.22), residues: 544 sheet: 0.46 (0.35), residues: 226 loop : -0.80 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.012 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.008 0.001 TRP N 199 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00379 (16474) covalent geometry : angle 0.60012 (23521) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.18741 ( 8) hydrogen bonds : bond 0.04144 ( 796) hydrogen bonds : angle 3.27936 ( 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 225 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8854 (mmm) cc_final: 0.8618 (mmp) REVERT: B 22 LEU cc_start: 0.8700 (mp) cc_final: 0.8429 (mt) REVERT: B 44 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8288 (mttp) REVERT: B 79 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8592 (mttm) REVERT: C 91 GLU cc_start: 0.8822 (tp30) cc_final: 0.8378 (tp30) REVERT: D 39 TYR cc_start: 0.8242 (t80) cc_final: 0.7330 (t80) REVERT: D 68 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7978 (mt-10) REVERT: E 39 HIS cc_start: 0.6747 (t70) cc_final: 0.6305 (t70) REVERT: E 54 TYR cc_start: 0.8923 (m-80) cc_final: 0.8666 (m-80) REVERT: E 90 MET cc_start: 0.8743 (mmm) cc_final: 0.8442 (tpp) REVERT: G 90 ASP cc_start: 0.8859 (t0) cc_final: 0.8438 (t0) REVERT: H 60 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (m110) REVERT: M 34 VAL cc_start: 0.7870 (t) cc_final: 0.7633 (p) REVERT: N 84 GLU cc_start: 0.7995 (tp30) cc_final: 0.7684 (mp0) REVERT: N 95 ASP cc_start: 0.8405 (t70) cc_final: 0.8001 (t70) REVERT: N 104 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7854 (mm-30) REVERT: N 111 GLU cc_start: 0.9177 (pt0) cc_final: 0.8875 (pp20) REVERT: N 237 GLU cc_start: 0.7708 (pm20) cc_final: 0.7484 (pm20) outliers start: 25 outliers final: 7 residues processed: 212 average time/residue: 0.6833 time to fit residues: 157.0313 Evaluate side-chains 193 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 19 SER 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 39 SER Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 223 SER 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: 5.9990 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 64 ASN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066881 restraints weight = 30578.544| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.04 r_work: 0.2852 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4301 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= 0.213 Angle : 0.608 8.635 23529 Z= 0.351 Chirality : 0.038 0.172 2652 Planarity : 0.004 0.051 1948 Dihedral : 30.170 178.724 4573 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.72 % Allowed : 23.52 % 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 aren not related in a simple way. whole: 1.49 (0.25), residues: 1188 helix: 2.60 (0.22), residues: 542 sheet: 0.50 (0.36), residues: 226 loop : -0.94 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.012 0.001 TYR N 117 PHE 0.009 0.001 PHE A 67 TRP 0.009 0.001 TRP N 132 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00489 (16474) covalent geometry : angle 0.60724 (23521) SS BOND : bond 0.00513 ( 4) SS BOND : angle 1.36396 ( 8) hydrogen bonds : bond 0.04432 ( 796) hydrogen bonds : angle 3.36460 ( 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 222 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8936 (mmm) cc_final: 0.8684 (mmp) REVERT: B 22 LEU cc_start: 0.8644 (mp) cc_final: 0.8384 (mt) REVERT: B 44 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8340 (mttm) REVERT: B 79 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8609 (mttm) REVERT: C 13 LYS cc_start: 0.8392 (tptt) cc_final: 0.8086 (tppp) REVERT: C 91 GLU cc_start: 0.8900 (tp30) cc_final: 0.8213 (tp30) REVERT: D 39 TYR cc_start: 0.8261 (t80) cc_final: 0.7344 (t80) REVERT: D 68 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7943 (mt-10) REVERT: D 105 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8386 (tttp) REVERT: E 54 TYR cc_start: 0.8943 (m-80) cc_final: 0.8701 (m-80) REVERT: E 90 MET cc_start: 0.8842 (mmm) cc_final: 0.8558 (tpp) REVERT: G 90 ASP cc_start: 0.8725 (t0) cc_final: 0.8251 (t0) REVERT: M 34 VAL cc_start: 0.8283 (t) cc_final: 0.7961 (p) REVERT: N 32 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7916 (mm-30) REVERT: N 95 ASP cc_start: 0.8576 (t70) cc_final: 0.8174 (t70) REVERT: N 104 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7980 (mm-30) REVERT: N 111 GLU cc_start: 0.9206 (pt0) cc_final: 0.8814 (pp20) REVERT: N 161 LYS cc_start: 0.9283 (ttpp) cc_final: 0.9009 (tptp) REVERT: N 162 MET cc_start: 0.8580 (mmm) cc_final: 0.7852 (mmm) REVERT: N 172 SER cc_start: 0.8273 (t) cc_final: 0.7994 (m) REVERT: N 240 ASP cc_start: 0.9049 (m-30) cc_final: 0.8655 (m-30) REVERT: N 251 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8412 (mp0) outliers start: 28 outliers final: 12 residues processed: 210 average time/residue: 0.8319 time to fit residues: 188.0628 Evaluate side-chains 195 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 159 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 170 HIS Chi-restraints excluded: chain N residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 112 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.106574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069752 restraints weight = 30869.544| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.04 r_work: 0.2921 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4556 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= 0.139 Angle : 0.567 8.367 23529 Z= 0.330 Chirality : 0.035 0.154 2652 Planarity : 0.004 0.039 1948 Dihedral : 29.768 179.489 4573 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 24.30 % 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 aren not related in a simple way. whole: 1.69 (0.25), residues: 1188 helix: 2.80 (0.22), residues: 543 sheet: 0.52 (0.36), residues: 226 loop : -0.85 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 176 TYR 0.011 0.001 TYR H 37 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP N 58 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00304 (16474) covalent geometry : angle 0.56712 (23521) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.24536 ( 8) hydrogen bonds : bond 0.03894 ( 796) hydrogen bonds : angle 3.17919 ( 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 222 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8594 (pt0) cc_final: 0.8099 (pm20) REVERT: B 22 LEU cc_start: 0.8670 (mp) cc_final: 0.8137 (mt) REVERT: B 23 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8057 (tpp80) REVERT: B 44 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8263 (mttm) REVERT: B 79 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8653 (mttm) REVERT: C 13 LYS cc_start: 0.8387 (tptt) cc_final: 0.8041 (tptp) REVERT: C 90 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8591 (t70) REVERT: D 39 TYR cc_start: 0.8201 (t80) cc_final: 0.7262 (t80) REVERT: D 68 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8018 (mt-10) REVERT: E 39 HIS cc_start: 0.6911 (t70) cc_final: 0.6485 (t70) REVERT: E 54 TYR cc_start: 0.8934 (m-80) cc_final: 0.8683 (m-80) REVERT: E 90 MET cc_start: 0.8792 (mmm) cc_final: 0.8504 (tpp) REVERT: G 90 ASP cc_start: 0.8680 (t0) cc_final: 0.8210 (t0) REVERT: H 56 MET cc_start: 0.9216 (tpp) cc_final: 0.8843 (tpp) REVERT: H 60 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8584 (m110) REVERT: M 34 VAL cc_start: 0.8298 (t) cc_final: 0.7976 (p) REVERT: M 45 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8321 (tptt) REVERT: M 95 ASP cc_start: 0.7825 (t0) cc_final: 0.7587 (t0) REVERT: M 112 ASP cc_start: 0.8227 (t0) cc_final: 0.7588 (m-30) REVERT: N 32 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7967 (mm-30) REVERT: N 84 GLU cc_start: 0.8170 (tp30) cc_final: 0.7911 (mp0) REVERT: N 95 ASP cc_start: 0.8587 (t70) cc_final: 0.8185 (t0) REVERT: N 103 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9240 (ttm) REVERT: N 104 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8009 (mm-30) REVERT: N 111 GLU cc_start: 0.9183 (pt0) cc_final: 0.8865 (pp20) REVERT: N 161 LYS cc_start: 0.9252 (ttpp) cc_final: 0.8940 (tptp) outliers start: 20 outliers final: 9 residues processed: 213 average time/residue: 0.7710 time to fit residues: 177.4565 Evaluate side-chains 196 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 90 ASP 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 45 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 170 HIS 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: 6.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068234 restraints weight = 30745.253| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.04 r_work: 0.2899 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16478 Z= 0.170 Angle : 0.577 8.238 23529 Z= 0.333 Chirality : 0.036 0.142 2652 Planarity : 0.004 0.037 1948 Dihedral : 29.759 178.590 4573 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.53 % Allowed : 25.07 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.25), residues: 1188 helix: 2.76 (0.22), residues: 543 sheet: 0.54 (0.36), residues: 226 loop : -0.83 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.015 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 132 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00387 (16474) covalent geometry : angle 0.57645 (23521) SS BOND : bond 0.00366 ( 4) SS BOND : angle 1.12335 ( 8) hydrogen bonds : bond 0.04047 ( 796) hydrogen bonds : angle 3.20317 ( 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: 26 poor density : 194 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8621 (pt0) cc_final: 0.8155 (pm20) REVERT: B 22 LEU cc_start: 0.8538 (mp) cc_final: 0.7949 (mt) REVERT: B 44 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8251 (mttm) REVERT: B 79 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8599 (mttm) REVERT: C 56 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: C 90 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8570 (t70) REVERT: D 30 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7658 (mmm-85) REVERT: D 39 TYR cc_start: 0.8205 (t80) cc_final: 0.7265 (t80) REVERT: D 68 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7946 (mt-10) REVERT: E 39 HIS cc_start: 0.6924 (t70) cc_final: 0.6495 (t70) REVERT: E 54 TYR cc_start: 0.8942 (m-80) cc_final: 0.8683 (m-80) REVERT: E 90 MET cc_start: 0.8768 (mmm) cc_final: 0.8479 (tpp) REVERT: E 97 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: G 90 ASP cc_start: 0.8641 (t0) cc_final: 0.8165 (t0) REVERT: H 60 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8605 (m110) REVERT: M 34 VAL cc_start: 0.8269 (t) cc_final: 0.7930 (p) REVERT: M 45 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8372 (tptt) REVERT: M 95 ASP cc_start: 0.7861 (t0) cc_final: 0.7573 (t70) REVERT: M 112 ASP cc_start: 0.8400 (t0) cc_final: 0.7787 (m-30) REVERT: M 176 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8353 (ttm110) REVERT: M 219 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8066 (mtm110) REVERT: M 234 ASN cc_start: 0.8079 (p0) cc_final: 0.7438 (m-40) REVERT: N 32 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8012 (mm-30) REVERT: N 95 ASP cc_start: 0.8515 (t70) cc_final: 0.8111 (t0) REVERT: N 104 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8067 (mm-30) REVERT: N 111 GLU cc_start: 0.9180 (pt0) cc_final: 0.8896 (pp20) outliers start: 26 outliers final: 9 residues processed: 207 average time/residue: 0.8498 time to fit residues: 189.3996 Evaluate side-chains 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 97 GLU 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 39 SER Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067752 restraints weight = 30460.336| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.01 r_work: 0.2889 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16478 Z= 0.181 Angle : 0.579 9.570 23529 Z= 0.333 Chirality : 0.036 0.144 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.620 178.241 4573 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 25.56 % Favored : 71.91 % 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 aren not related in a simple way. whole: 1.61 (0.25), residues: 1188 helix: 2.70 (0.22), residues: 543 sheet: 0.48 (0.36), residues: 218 loop : -0.80 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.014 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.001 TRP M 132 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00413 (16474) covalent geometry : angle 0.57884 (23521) SS BOND : bond 0.00424 ( 4) SS BOND : angle 1.09447 ( 8) hydrogen bonds : bond 0.04125 ( 796) hydrogen bonds : angle 3.26247 ( 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 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8625 (pt0) cc_final: 0.8180 (pm20) REVERT: B 44 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8334 (mttm) REVERT: B 79 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8689 (mttm) REVERT: C 56 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: D 39 TYR cc_start: 0.8312 (t80) cc_final: 0.7370 (t80) REVERT: D 68 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8009 (mt-10) REVERT: E 39 HIS cc_start: 0.6889 (t70) cc_final: 0.6466 (t70) REVERT: E 54 TYR cc_start: 0.8970 (m-80) cc_final: 0.8707 (m-80) REVERT: E 59 GLU cc_start: 0.8548 (pm20) cc_final: 0.8339 (pm20) REVERT: E 90 MET cc_start: 0.8774 (mmm) cc_final: 0.8489 (tpp) REVERT: E 97 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: E 115 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8876 (mtmm) REVERT: F 53 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8233 (tp30) REVERT: G 90 ASP cc_start: 0.8625 (t0) cc_final: 0.8156 (t0) REVERT: H 60 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8629 (m110) REVERT: M 34 VAL cc_start: 0.8400 (t) cc_final: 0.7991 (p) REVERT: M 45 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8372 (tptt) REVERT: M 95 ASP cc_start: 0.7935 (t0) cc_final: 0.7636 (t70) REVERT: M 112 ASP cc_start: 0.8346 (t0) cc_final: 0.7927 (m-30) REVERT: M 234 ASN cc_start: 0.7917 (p0) cc_final: 0.7535 (m-40) REVERT: N 95 ASP cc_start: 0.8534 (t70) cc_final: 0.8111 (t0) REVERT: N 237 GLU cc_start: 0.7707 (pm20) cc_final: 0.7200 (mp0) outliers start: 26 outliers final: 13 residues processed: 201 average time/residue: 0.8075 time to fit residues: 175.2573 Evaluate side-chains 192 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 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 D residue 29 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 48 ASP 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 39 SER Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 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: 0.1980 chunk 104 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068566 restraints weight = 30807.736| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.05 r_work: 0.2899 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4949 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= 0.149 Angle : 0.577 10.115 23529 Z= 0.331 Chirality : 0.035 0.147 2652 Planarity : 0.004 0.048 1948 Dihedral : 29.586 178.116 4573 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.04 % Allowed : 26.24 % Favored : 71.72 % 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 aren not related in a simple way. whole: 1.67 (0.25), residues: 1188 helix: 2.74 (0.22), residues: 543 sheet: 0.50 (0.36), residues: 218 loop : -0.77 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 176 TYR 0.013 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00335 (16474) covalent geometry : angle 0.57670 (23521) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.87231 ( 8) hydrogen bonds : bond 0.03971 ( 796) hydrogen bonds : angle 3.22435 ( 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 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8611 (pt0) cc_final: 0.8098 (pm20) REVERT: B 44 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8311 (mttm) REVERT: B 79 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8689 (mttm) REVERT: C 56 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: D 39 TYR cc_start: 0.8273 (t80) cc_final: 0.7329 (t80) REVERT: D 68 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8016 (mt-10) REVERT: E 39 HIS cc_start: 0.6871 (t70) cc_final: 0.6447 (t70) REVERT: E 54 TYR cc_start: 0.8951 (m-80) cc_final: 0.8700 (m-80) REVERT: E 59 GLU cc_start: 0.8535 (pm20) cc_final: 0.8335 (pm20) REVERT: E 90 MET cc_start: 0.8741 (mmm) cc_final: 0.8444 (tpp) REVERT: E 97 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: E 115 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8854 (mtmm) REVERT: F 44 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8338 (mttm) REVERT: F 53 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8183 (tp30) REVERT: G 90 ASP cc_start: 0.8595 (t0) cc_final: 0.8165 (t0) REVERT: H 60 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8605 (m110) REVERT: M 34 VAL cc_start: 0.8373 (t) cc_final: 0.7973 (p) REVERT: M 45 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8355 (tptt) REVERT: M 95 ASP cc_start: 0.7935 (t0) cc_final: 0.7614 (t70) REVERT: M 112 ASP cc_start: 0.8358 (t0) cc_final: 0.7906 (m-30) REVERT: M 176 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8222 (ttm110) REVERT: M 219 ARG cc_start: 0.8597 (mtp180) cc_final: 0.7956 (ttp-110) REVERT: M 234 ASN cc_start: 0.7984 (p0) cc_final: 0.7662 (m-40) REVERT: N 95 ASP cc_start: 0.8526 (t70) cc_final: 0.8106 (t0) REVERT: N 237 GLU cc_start: 0.7770 (pm20) cc_final: 0.7220 (mp0) outliers start: 21 outliers final: 10 residues processed: 199 average time/residue: 0.7708 time to fit residues: 165.1399 Evaluate side-chains 196 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 97 GLU 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 42 MET Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 119 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN M 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066303 restraints weight = 30690.687| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.03 r_work: 0.2839 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16478 Z= 0.230 Angle : 0.611 10.592 23529 Z= 0.348 Chirality : 0.038 0.145 2652 Planarity : 0.004 0.038 1948 Dihedral : 29.814 177.854 4573 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.85 % Allowed : 26.82 % Favored : 71.33 % 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 aren not related in a simple way. whole: 1.48 (0.25), residues: 1188 helix: 2.58 (0.22), residues: 543 sheet: 0.35 (0.36), residues: 220 loop : -0.81 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 176 TYR 0.015 0.001 TYR H 37 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP M 132 HIS 0.005 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00532 (16474) covalent geometry : angle 0.61102 (23521) SS BOND : bond 0.00535 ( 4) SS BOND : angle 1.15111 ( 8) hydrogen bonds : bond 0.04415 ( 796) hydrogen bonds : angle 3.35921 ( 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 200 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8637 (pt0) cc_final: 0.8185 (pm20) REVERT: B 22 LEU cc_start: 0.8520 (mp) cc_final: 0.8218 (mt) REVERT: B 44 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8353 (mttm) REVERT: C 56 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8582 (tt0) REVERT: D 39 TYR cc_start: 0.8394 (t80) cc_final: 0.7491 (t80) REVERT: E 39 HIS cc_start: 0.6874 (t70) cc_final: 0.6506 (t70) REVERT: E 54 TYR cc_start: 0.8993 (m-80) cc_final: 0.8740 (m-80) REVERT: E 59 GLU cc_start: 0.8603 (pm20) cc_final: 0.8393 (pm20) REVERT: E 90 MET cc_start: 0.8814 (mmm) cc_final: 0.8504 (tpp) REVERT: E 97 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: E 115 LYS cc_start: 0.9177 (mtpp) cc_final: 0.8901 (mtmm) REVERT: F 44 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8462 (mtmm) REVERT: F 53 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8228 (tp30) REVERT: G 90 ASP cc_start: 0.8686 (t0) cc_final: 0.8228 (t0) REVERT: H 60 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8723 (m-40) REVERT: M 34 VAL cc_start: 0.8461 (t) cc_final: 0.8069 (p) REVERT: M 45 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8442 (tptt) REVERT: M 95 ASP cc_start: 0.8039 (t0) cc_final: 0.7712 (t70) REVERT: M 112 ASP cc_start: 0.8350 (t0) cc_final: 0.7999 (m-30) REVERT: M 234 ASN cc_start: 0.7997 (p0) cc_final: 0.7349 (m-40) REVERT: N 32 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7826 (mm-30) REVERT: N 95 ASP cc_start: 0.8555 (t70) cc_final: 0.8139 (t0) outliers start: 19 outliers final: 13 residues processed: 192 average time/residue: 0.8688 time to fit residues: 178.9533 Evaluate side-chains 196 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain E residue 97 GLU 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 48 ASP Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.105349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068236 restraints weight = 30580.215| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.03 r_work: 0.2882 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5066 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= 0.145 Angle : 0.587 10.326 23529 Z= 0.336 Chirality : 0.035 0.147 2652 Planarity : 0.004 0.047 1948 Dihedral : 29.654 178.539 4573 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.65 % Allowed : 26.82 % 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 aren not related in a simple way. whole: 1.60 (0.25), residues: 1188 helix: 2.66 (0.22), residues: 543 sheet: 0.41 (0.36), residues: 218 loop : -0.72 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 176 TYR 0.014 0.001 TYR H 37 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00321 (16474) covalent geometry : angle 0.58693 (23521) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.98389 ( 8) hydrogen bonds : bond 0.03973 ( 796) hydrogen bonds : angle 3.27151 ( 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 201 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8586 (pt0) cc_final: 0.8158 (pm20) REVERT: B 22 LEU cc_start: 0.8450 (mp) cc_final: 0.8108 (mt) REVERT: B 44 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8348 (mttm) REVERT: C 56 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: D 39 TYR cc_start: 0.8213 (t80) cc_final: 0.7265 (t80) REVERT: D 68 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7943 (mt-10) REVERT: E 39 HIS cc_start: 0.6885 (t70) cc_final: 0.6506 (t70) REVERT: E 54 TYR cc_start: 0.8961 (m-80) cc_final: 0.8717 (m-80) REVERT: E 59 GLU cc_start: 0.8585 (pm20) cc_final: 0.8379 (pm20) REVERT: E 90 MET cc_start: 0.8711 (mmm) cc_final: 0.8432 (tpp) REVERT: E 97 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: E 115 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8874 (mtmm) REVERT: F 44 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8404 (mtmm) REVERT: F 53 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8207 (tp30) REVERT: G 90 ASP cc_start: 0.8575 (t0) cc_final: 0.8195 (t0) REVERT: H 60 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8572 (m110) REVERT: M 34 VAL cc_start: 0.8418 (t) cc_final: 0.8040 (p) REVERT: M 45 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (tptt) REVERT: M 95 ASP cc_start: 0.8020 (t0) cc_final: 0.7696 (t70) REVERT: M 112 ASP cc_start: 0.8322 (t0) cc_final: 0.7937 (m-30) REVERT: M 234 ASN cc_start: 0.7892 (p0) cc_final: 0.7189 (m-40) REVERT: N 32 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7818 (mm-30) REVERT: N 95 ASP cc_start: 0.8524 (t70) cc_final: 0.8093 (t0) outliers start: 17 outliers final: 9 residues processed: 195 average time/residue: 0.8674 time to fit residues: 181.2954 Evaluate side-chains 192 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain E residue 97 GLU 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 45 LYS Chi-restraints excluded: chain M residue 65 GLN Chi-restraints excluded: chain M residue 173 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 105 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.105076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067984 restraints weight = 30387.181| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.02 r_work: 0.2890 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16478 Z= 0.202 Angle : 0.771 59.199 23529 Z= 0.464 Chirality : 0.038 0.537 2652 Planarity : 0.005 0.064 1948 Dihedral : 29.649 178.602 4573 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.46 % Allowed : 27.41 % Favored : 71.14 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 1.56 (0.25), residues: 1188 helix: 2.62 (0.22), residues: 543 sheet: 0.40 (0.36), residues: 218 loop : -0.75 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 23 TYR 0.014 0.001 TYR H 37 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP N 58 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00443 (16474) covalent geometry : angle 0.77089 (23521) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.03174 ( 8) hydrogen bonds : bond 0.04046 ( 796) hydrogen bonds : angle 3.26845 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5770.30 seconds wall clock time: 98 minutes 53.35 seconds (5933.35 seconds total)