Starting phenix.real_space_refine on Fri Jul 3 20:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sps_40683/07_2026/8sps_40683.map" } resolution = 3.0 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= 0.003 sd= 0.051 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 37 5.16 5 C 9478 2.51 5 N 2996 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16515 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3055 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2972 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" 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: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 373 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.46, per 1000 atoms: 0.21 Number of scatterers: 16515 At special positions: 0 Unit cell: (139.392, 145.728, 157.344, 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 37 16.00 P 294 15.00 O 3710 8.00 N 2996 7.00 C 9478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 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: 1.33 Conformation dependent library (CDL) restraints added in 387.5 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 50.6% alpha, 17.9% beta 139 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'L' and resid 140 through 161 removed outlier: 4.105A pdb=" N LYS L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU L 152 " --> pdb=" O GLN L 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 Processing helix chain 'L' and resid 180 through 189 removed outlier: 3.520A pdb=" N GLU L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 214 Proline residue: L 202 - end of helix Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.592A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.803A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A 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 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.548A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 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: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.511A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (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 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.673A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.709A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing helix chain 'M' and resid 240 through 247 Processing helix chain 'M' and resid 255 through 268 removed outlier: 3.586A pdb=" N HIS M 262 " --> pdb=" O GLN M 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN M 265 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN M 266 " --> pdb=" O HIS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 287 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A 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: 6.573A 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: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (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 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.955A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.817A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4862 1.36 - 1.51: 7352 1.51 - 1.67: 5139 1.67 - 1.83: 57 Bond restraints: 17425 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.191 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.06e+02 bond pdb=" C ASN C 94 " pdb=" O ASN C 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.65e+02 bond pdb=" CA MET C 51 " pdb=" C MET C 51 " ideal model delta sigma weight residual 1.523 1.362 0.161 1.37e-02 5.33e+03 1.38e+02 ... (remaining 17420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 24738 5.95 - 11.91: 56 11.91 - 17.86: 9 17.86 - 23.82: 1 23.82 - 29.77: 1 Bond angle restraints: 24805 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.90 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.93 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 128.73 -17.93 2.13e+00 2.20e-01 7.09e+01 angle pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 121.54 134.08 -12.54 1.91e+00 2.74e-01 4.31e+01 angle pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " pdb=" CG GLN B 93 " ideal model delta sigma weight residual 114.10 101.79 12.31 2.00e+00 2.50e-01 3.79e+01 ... (remaining 24800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8097 35.44 - 70.87: 1595 70.87 - 106.31: 36 106.31 - 141.74: 0 141.74 - 177.18: 2 Dihedral angle restraints: 9730 sinusoidal: 5861 harmonic: 3869 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.50 -14.10 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.44 11.84 0 2.50e+00 1.60e-01 2.24e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2760 0.137 - 0.273: 29 0.273 - 0.410: 6 0.410 - 0.547: 2 0.547 - 0.684: 2 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CG LEU C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2796 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " 0.035 2.00e-02 2.50e+03 7.34e-02 5.39e+01 pdb=" C GLU C 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET C 51 " 0.092 2.00e-02 2.50e+03 pdb=" O MET C 51 " -0.035 2.00e-02 2.50e+03 pdb=" N ALA C 52 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO N 63 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.067 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 3 1.44 - 2.30: 8 2.30 - 3.17: 12600 3.17 - 4.03: 48048 4.03 - 4.90: 81529 Warning: very small nonbonded interaction distances. Nonbonded interactions: 142188 Sorted by model distance: nonbonded pdb=" O TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.574 3.120 nonbonded pdb=" C TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.937 3.350 nonbonded pdb=" O TYR L 162 " pdb=" CE LYS G 13 " model vdw 1.305 3.440 nonbonded pdb=" N THR L 163 " pdb=" NZ LYS G 13 " model vdw 1.818 3.200 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 3.040 ... (remaining 142183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) } 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: 0.910 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.870 Find NCS groups from input model: 0.180 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.009 0.191 17429 Z= 0.644 Angle : 0.972 29.772 24813 Z= 0.699 Chirality : 0.055 0.684 2799 Planarity : 0.007 0.127 2116 Dihedral : 27.009 177.177 7234 Min Nonbonded Distance : 0.574 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 0.53 % Allowed : 21.53 % Favored : 77.94 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1306 helix: -0.09 (0.18), residues: 634 sheet: -0.23 (0.34), residues: 234 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 100 TYR 0.045 0.002 TYR H 41 PHE 0.029 0.002 PHE A 78 TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.64 (17425) covalent geometry : angle 0.97176 / 0.70 (24805) SS BOND : bond 0.00293 / 0.17 ( 4) SS BOND : angle 1.22539 / 2.21 ( 8) hydrogen bonds : bond 0.13037 / 14.07 ( 950) hydrogen bonds : angle 5.39350 / 7.17 ( 2434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 360 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8364 (m110) cc_final: 0.7835 (m-40) REVERT: H 84 TYR cc_start: 0.8585 (m-10) cc_final: 0.8108 (m-10) outliers start: 6 outliers final: 2 residues processed: 362 average time/residue: 0.6308 time to fit residues: 250.0830 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain K residue 264 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 31 HIS C 38 ASN C 73 ASN D 85 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 50 HIS H 96 GLN K 57 GLN K 196 GLN K 234 ASN N 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.128041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081087 restraints weight = 38271.630| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.67 r_work: 0.3080 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17429 Z= 0.162 Angle : 0.686 8.477 24813 Z= 0.383 Chirality : 0.046 0.246 2799 Planarity : 0.006 0.082 2116 Dihedral : 29.960 172.113 4697 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.94 % Allowed : 26.78 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.22), residues: 1306 helix: 1.35 (0.19), residues: 647 sheet: -0.11 (0.33), residues: 234 loop : -1.00 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 87 TYR 0.023 0.001 TYR N 245 PHE 0.008 0.001 PHE N 256 TRP 0.010 0.001 TRP N 199 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (17425) covalent geometry : angle 0.68626 / 0.38 (24805) SS BOND : bond 0.00395 / 0.21 ( 4) SS BOND : angle 1.17712 / 1.98 ( 8) hydrogen bonds : bond 0.05206 / 5.56 ( 950) hydrogen bonds : angle 4.04291 / 5.48 ( 2434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: B 79 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8614 (mtmt) REVERT: C 15 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8103 (ptpp) REVERT: C 91 GLU cc_start: 0.8589 (tt0) cc_final: 0.8269 (tt0) REVERT: D 69 ASP cc_start: 0.9144 (t0) cc_final: 0.8885 (t0) REVERT: D 87 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7885 (mmm-85) REVERT: D 94 GLU cc_start: 0.9027 (mp0) cc_final: 0.8825 (mp0) REVERT: D 114 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9118 (mm-30) REVERT: E 83 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6515 (ptm-80) REVERT: F 22 LEU cc_start: 0.8811 (mt) cc_final: 0.8574 (mt) REVERT: F 25 ASN cc_start: 0.8635 (m110) cc_final: 0.8120 (m-40) REVERT: F 95 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7814 (mtp85) REVERT: G 73 ASN cc_start: 0.8702 (t0) cc_final: 0.8155 (m-40) REVERT: G 91 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: H 69 ASP cc_start: 0.8433 (t0) cc_final: 0.8213 (t0) REVERT: H 84 TYR cc_start: 0.8982 (m-10) cc_final: 0.8417 (m-10) REVERT: H 94 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: H 114 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8918 (mm-30) REVERT: K 32 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7687 (mm-30) REVERT: K 84 GLU cc_start: 0.9070 (tp30) cc_final: 0.8828 (tp30) REVERT: K 87 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8519 (ttpp) REVERT: K 95 ASP cc_start: 0.8065 (t0) cc_final: 0.7785 (t0) REVERT: K 111 GLU cc_start: 0.9348 (pm20) cc_final: 0.9080 (pm20) REVERT: K 176 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8323 (ttt90) REVERT: K 182 LYS cc_start: 0.8367 (tptt) cc_final: 0.8059 (tppt) REVERT: K 194 TYR cc_start: 0.7958 (m-80) cc_final: 0.7735 (m-80) REVERT: N 239 ASP cc_start: 0.8040 (m-30) cc_final: 0.7839 (t0) outliers start: 33 outliers final: 12 residues processed: 258 average time/residue: 0.6469 time to fit residues: 183.4823 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 249 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 0.0000 chunk 145 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 73 ASN G 31 HIS K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078193 restraints weight = 38564.745| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.68 r_work: 0.2987 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17429 Z= 0.185 Angle : 0.668 10.818 24813 Z= 0.371 Chirality : 0.044 0.207 2799 Planarity : 0.005 0.062 2116 Dihedral : 29.982 170.593 4693 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.80 % Allowed : 24.47 % Favored : 70.73 % 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: 1.05 (0.23), residues: 1306 helix: 2.03 (0.20), residues: 644 sheet: -0.04 (0.34), residues: 234 loop : -0.93 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 176 TYR 0.030 0.002 TYR D 84 PHE 0.017 0.001 PHE N 256 TRP 0.010 0.001 TRP L 207 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (17425) covalent geometry : angle 0.66774 / 0.37 (24805) SS BOND : bond 0.00484 / 0.23 ( 4) SS BOND : angle 0.96949 / 1.67 ( 8) hydrogen bonds : bond 0.04805 / 5.14 ( 950) hydrogen bonds : angle 3.71904 / 5.09 ( 2434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8703 (mtmt) REVERT: C 71 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8211 (ttp80) REVERT: C 91 GLU cc_start: 0.8598 (tt0) cc_final: 0.8232 (tt0) REVERT: D 69 ASP cc_start: 0.9116 (t0) cc_final: 0.8759 (t0) REVERT: D 94 GLU cc_start: 0.9044 (mp0) cc_final: 0.8764 (mp0) REVERT: D 100 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8759 (mpt-90) REVERT: D 114 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9004 (mm-30) REVERT: E 73 GLU cc_start: 0.8669 (tt0) cc_final: 0.8108 (tt0) REVERT: E 90 MET cc_start: 0.8715 (tpp) cc_final: 0.8233 (mmp) REVERT: F 25 ASN cc_start: 0.8511 (m110) cc_final: 0.7948 (m-40) REVERT: G 20 ARG cc_start: 0.8551 (mtt90) cc_final: 0.8177 (mtm-85) REVERT: G 64 GLU cc_start: 0.9060 (tt0) cc_final: 0.8799 (tt0) REVERT: G 73 ASN cc_start: 0.8744 (t0) cc_final: 0.8119 (m-40) REVERT: G 75 LYS cc_start: 0.8555 (mttm) cc_final: 0.8259 (mmmm) REVERT: G 91 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: G 92 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8039 (mt-10) REVERT: H 47 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8814 (mptp) REVERT: H 52 ASP cc_start: 0.8522 (m-30) cc_final: 0.8007 (t0) REVERT: H 69 ASP cc_start: 0.8832 (t0) cc_final: 0.8545 (t0) REVERT: H 84 TYR cc_start: 0.8937 (m-10) cc_final: 0.8472 (m-10) REVERT: H 114 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8869 (mm-30) REVERT: K 32 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7978 (mm-30) REVERT: K 84 GLU cc_start: 0.9142 (tp30) cc_final: 0.8808 (tp30) REVERT: K 87 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8562 (ttpp) REVERT: K 95 ASP cc_start: 0.8097 (t0) cc_final: 0.7631 (t0) REVERT: K 103 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.7638 (tmm) REVERT: K 111 GLU cc_start: 0.9312 (pm20) cc_final: 0.9070 (pm20) REVERT: K 176 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8041 (tpt-90) REVERT: K 182 LYS cc_start: 0.8492 (tptt) cc_final: 0.8271 (tppt) REVERT: K 214 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: K 237 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7344 (tm-30) REVERT: K 239 ASP cc_start: 0.8773 (t0) cc_final: 0.8057 (t0) REVERT: N 95 ASP cc_start: 0.8397 (t0) cc_final: 0.8156 (t0) REVERT: N 108 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7129 (pp) REVERT: N 120 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: N 263 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8840 (pm20) outliers start: 54 outliers final: 18 residues processed: 260 average time/residue: 0.7057 time to fit residues: 200.6677 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 120 ARG Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 73 ASN E 39 HIS K 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.124394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076346 restraints weight = 38259.859| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.78 r_work: 0.2966 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17429 Z= 0.171 Angle : 0.649 10.207 24813 Z= 0.359 Chirality : 0.043 0.203 2799 Planarity : 0.005 0.072 2116 Dihedral : 29.935 169.361 4693 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.83 % Allowed : 27.14 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1306 helix: 2.24 (0.20), residues: 645 sheet: 0.01 (0.34), residues: 234 loop : -0.97 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 87 TYR 0.031 0.002 TYR D 84 PHE 0.008 0.001 PHE N 256 TRP 0.010 0.001 TRP L 207 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (17425) covalent geometry : angle 0.64931 / 0.36 (24805) SS BOND : bond 0.00541 / 0.28 ( 4) SS BOND : angle 0.83912 / 1.37 ( 8) hydrogen bonds : bond 0.04358 / 4.70 ( 950) hydrogen bonds : angle 3.61249 / 4.95 ( 2434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: B 25 ASN cc_start: 0.8869 (m-40) cc_final: 0.8559 (m-40) REVERT: B 79 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8772 (mtmt) REVERT: C 72 ASP cc_start: 0.7770 (m-30) cc_final: 0.7568 (m-30) REVERT: C 76 THR cc_start: 0.9011 (p) cc_final: 0.8599 (t) REVERT: D 69 ASP cc_start: 0.9131 (t0) cc_final: 0.8764 (t0) REVERT: D 87 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8175 (mmt-90) REVERT: D 94 GLU cc_start: 0.9035 (mp0) cc_final: 0.8745 (mp0) REVERT: E 59 GLU cc_start: 0.8680 (pm20) cc_final: 0.8394 (pm20) REVERT: E 73 GLU cc_start: 0.8666 (tt0) cc_final: 0.7994 (tt0) REVERT: E 90 MET cc_start: 0.8760 (tpp) cc_final: 0.8304 (mmp) REVERT: E 123 ASP cc_start: 0.8594 (m-30) cc_final: 0.8101 (m-30) REVERT: F 25 ASN cc_start: 0.8488 (m110) cc_final: 0.7873 (m-40) REVERT: F 95 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7909 (mtp85) REVERT: G 73 ASN cc_start: 0.8830 (t0) cc_final: 0.8371 (m-40) REVERT: G 75 LYS cc_start: 0.8684 (mttm) cc_final: 0.8443 (mmmm) REVERT: G 91 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: H 47 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8830 (mptm) REVERT: H 69 ASP cc_start: 0.8827 (t0) cc_final: 0.8527 (t0) REVERT: H 84 TYR cc_start: 0.8897 (m-10) cc_final: 0.8538 (m-10) REVERT: H 114 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8782 (mm-30) REVERT: K 32 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8206 (mm-30) REVERT: K 84 GLU cc_start: 0.9190 (tp30) cc_final: 0.8860 (tp30) REVERT: K 87 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8641 (ttpp) REVERT: K 95 ASP cc_start: 0.8173 (t0) cc_final: 0.7707 (t0) REVERT: K 103 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.7774 (tmm) REVERT: K 111 GLU cc_start: 0.9313 (pm20) cc_final: 0.9068 (pm20) REVERT: K 176 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8299 (tpt-90) REVERT: K 182 LYS cc_start: 0.8597 (tptt) cc_final: 0.8319 (tppt) REVERT: N 95 ASP cc_start: 0.8314 (t0) cc_final: 0.8001 (t0) REVERT: N 103 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8172 (ttp) REVERT: N 108 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7028 (pp) REVERT: N 112 ASP cc_start: 0.8017 (m-30) cc_final: 0.7804 (m-30) REVERT: N 130 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8588 (p0) REVERT: N 169 MET cc_start: 0.8823 (mmm) cc_final: 0.8558 (mmp) REVERT: N 263 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8686 (pm20) outliers start: 43 outliers final: 18 residues processed: 240 average time/residue: 0.6824 time to fit residues: 179.2814 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 125 GLN C 38 ASN C 73 ASN E 108 ASN H 50 HIS K 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076162 restraints weight = 38127.935| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.48 r_work: 0.2962 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17429 Z= 0.163 Angle : 0.646 12.200 24813 Z= 0.357 Chirality : 0.043 0.206 2799 Planarity : 0.005 0.053 2116 Dihedral : 29.913 169.613 4693 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.09 % Allowed : 27.58 % Favored : 68.33 % 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 are not related in a simple way. whole: 1.36 (0.24), residues: 1306 helix: 2.37 (0.20), residues: 645 sheet: 0.04 (0.35), residues: 234 loop : -0.92 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 20 TYR 0.032 0.001 TYR A 41 PHE 0.007 0.001 PHE E 67 TRP 0.009 0.001 TRP L 207 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17425) covalent geometry : angle 0.64611 / 0.36 (24805) SS BOND : bond 0.00422 / 0.21 ( 4) SS BOND : angle 0.79963 / 1.33 ( 8) hydrogen bonds : bond 0.04272 / 4.60 ( 950) hydrogen bonds : angle 3.54917 / 4.87 ( 2434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: L 197 MET cc_start: 0.3223 (mmm) cc_final: 0.2554 (mpt) REVERT: A 105 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: A 133 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6999 (mt-10) REVERT: B 25 ASN cc_start: 0.8831 (m-40) cc_final: 0.8540 (m-40) REVERT: B 79 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8805 (mtmt) REVERT: C 76 THR cc_start: 0.9043 (p) cc_final: 0.8669 (t) REVERT: D 69 ASP cc_start: 0.9115 (t0) cc_final: 0.8737 (t0) REVERT: D 87 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8276 (mmm-85) REVERT: D 94 GLU cc_start: 0.9026 (mp0) cc_final: 0.8668 (mp0) REVERT: E 73 GLU cc_start: 0.8740 (tt0) cc_final: 0.7967 (tt0) REVERT: E 90 MET cc_start: 0.8729 (tpp) cc_final: 0.8162 (mmp) REVERT: E 123 ASP cc_start: 0.8665 (m-30) cc_final: 0.8212 (m-30) REVERT: F 25 ASN cc_start: 0.8483 (m110) cc_final: 0.7856 (m-40) REVERT: G 64 GLU cc_start: 0.9139 (tt0) cc_final: 0.8851 (tt0) REVERT: G 73 ASN cc_start: 0.8857 (t0) cc_final: 0.8396 (m-40) REVERT: G 75 LYS cc_start: 0.8736 (mttm) cc_final: 0.8508 (mmmm) REVERT: G 91 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: H 47 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8834 (mptm) REVERT: H 69 ASP cc_start: 0.8955 (t0) cc_final: 0.8637 (t0) REVERT: H 84 TYR cc_start: 0.8966 (m-10) cc_final: 0.8558 (m-10) REVERT: H 86 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9153 (mmtp) REVERT: H 114 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8805 (mm-30) REVERT: K 84 GLU cc_start: 0.9180 (tp30) cc_final: 0.8906 (tp30) REVERT: K 87 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8719 (ttpp) REVERT: K 95 ASP cc_start: 0.8216 (t0) cc_final: 0.7738 (t0) REVERT: K 111 GLU cc_start: 0.9248 (pm20) cc_final: 0.9025 (pm20) REVERT: K 176 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8326 (tpt-90) REVERT: K 182 LYS cc_start: 0.8586 (tptt) cc_final: 0.8342 (tppt) REVERT: K 237 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7295 (tm-30) REVERT: K 239 ASP cc_start: 0.8782 (t0) cc_final: 0.8164 (t0) REVERT: N 95 ASP cc_start: 0.8219 (t0) cc_final: 0.7884 (t0) REVERT: N 103 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: N 108 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7005 (pp) REVERT: N 112 ASP cc_start: 0.7967 (m-30) cc_final: 0.7739 (m-30) REVERT: N 177 VAL cc_start: 0.8460 (t) cc_final: 0.8000 (p) REVERT: N 263 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8765 (pm20) outliers start: 46 outliers final: 19 residues processed: 240 average time/residue: 0.6394 time to fit residues: 168.7596 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 153 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 0.0270 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 38 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.077269 restraints weight = 38162.822| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.47 r_work: 0.2992 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17429 Z= 0.131 Angle : 0.633 12.510 24813 Z= 0.352 Chirality : 0.042 0.205 2799 Planarity : 0.005 0.061 2116 Dihedral : 29.843 168.935 4693 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.38 % Allowed : 28.56 % Favored : 68.06 % 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: 1.47 (0.24), residues: 1306 helix: 2.46 (0.20), residues: 645 sheet: 0.09 (0.35), residues: 234 loop : -0.85 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.054 0.001 TYR D 84 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP L 207 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (17425) covalent geometry : angle 0.63291 / 0.35 (24805) SS BOND : bond 0.00329 / 0.18 ( 4) SS BOND : angle 0.76454 / 1.26 ( 8) hydrogen bonds : bond 0.03966 / 4.30 ( 950) hydrogen bonds : angle 3.45939 / 4.78 ( 2434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 197 MET cc_start: 0.3273 (mmm) cc_final: 0.2878 (mpt) REVERT: A 105 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: A 133 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: B 25 ASN cc_start: 0.8846 (m-40) cc_final: 0.8554 (m-40) REVERT: B 79 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8846 (mtmt) REVERT: C 76 THR cc_start: 0.9006 (p) cc_final: 0.8643 (t) REVERT: D 69 ASP cc_start: 0.9127 (t0) cc_final: 0.8758 (t0) REVERT: D 87 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8082 (mmt-90) REVERT: D 94 GLU cc_start: 0.8995 (mp0) cc_final: 0.8738 (mp0) REVERT: E 73 GLU cc_start: 0.8768 (tt0) cc_final: 0.8055 (tt0) REVERT: E 90 MET cc_start: 0.8659 (tpp) cc_final: 0.8096 (mmp) REVERT: E 123 ASP cc_start: 0.8651 (m-30) cc_final: 0.8278 (m-30) REVERT: F 25 ASN cc_start: 0.8483 (m110) cc_final: 0.7845 (m-40) REVERT: G 73 ASN cc_start: 0.8859 (t0) cc_final: 0.8480 (m-40) REVERT: G 75 LYS cc_start: 0.8726 (mttm) cc_final: 0.8496 (mmmm) REVERT: H 47 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8827 (mptp) REVERT: H 52 ASP cc_start: 0.8500 (m-30) cc_final: 0.7931 (t0) REVERT: H 69 ASP cc_start: 0.8877 (t0) cc_final: 0.8581 (t0) REVERT: H 84 TYR cc_start: 0.8967 (m-10) cc_final: 0.8539 (m-10) REVERT: H 114 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8820 (mm-30) REVERT: K 84 GLU cc_start: 0.9168 (tp30) cc_final: 0.8892 (tp30) REVERT: K 87 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8717 (ttpp) REVERT: K 95 ASP cc_start: 0.8221 (t0) cc_final: 0.7725 (t0) REVERT: K 111 GLU cc_start: 0.9236 (pm20) cc_final: 0.9017 (pm20) REVERT: K 176 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8237 (tpt-90) REVERT: K 237 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7292 (tm-30) REVERT: K 239 ASP cc_start: 0.8772 (t0) cc_final: 0.8167 (t0) REVERT: N 95 ASP cc_start: 0.8185 (t0) cc_final: 0.7840 (t0) REVERT: N 108 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.6809 (pp) REVERT: N 263 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8767 (pm20) outliers start: 38 outliers final: 15 residues processed: 239 average time/residue: 0.6529 time to fit residues: 171.3744 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 50.0000 chunk 62 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 38 ASN C 73 ASN D 96 GLN G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077355 restraints weight = 38019.257| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.53 r_work: 0.2997 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17429 Z= 0.131 Angle : 0.623 13.112 24813 Z= 0.348 Chirality : 0.042 0.209 2799 Planarity : 0.004 0.055 2116 Dihedral : 29.788 169.435 4693 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.94 % Allowed : 29.63 % Favored : 67.44 % 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: 1.55 (0.24), residues: 1306 helix: 2.51 (0.20), residues: 644 sheet: 0.15 (0.35), residues: 234 loop : -0.80 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 71 TYR 0.065 0.001 TYR D 84 PHE 0.007 0.001 PHE E 104 TRP 0.009 0.001 TRP N 58 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (17425) covalent geometry : angle 0.62269 / 0.35 (24805) SS BOND : bond 0.00275 / 0.14 ( 4) SS BOND : angle 0.69431 / 1.16 ( 8) hydrogen bonds : bond 0.03909 / 4.26 ( 950) hydrogen bonds : angle 3.43840 / 4.75 ( 2434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 197 MET cc_start: 0.3432 (mmm) cc_final: 0.2837 (mpt) REVERT: A 105 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: B 25 ASN cc_start: 0.8856 (m-40) cc_final: 0.8587 (m-40) REVERT: B 79 LYS cc_start: 0.9144 (mtmt) cc_final: 0.8849 (mtmt) REVERT: B 88 TYR cc_start: 0.8855 (m-80) cc_final: 0.8471 (m-80) REVERT: C 76 THR cc_start: 0.9003 (p) cc_final: 0.8637 (t) REVERT: C 91 GLU cc_start: 0.8586 (tt0) cc_final: 0.8380 (tt0) REVERT: D 69 ASP cc_start: 0.9121 (t0) cc_final: 0.8735 (t0) REVERT: D 87 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8177 (mmt-90) REVERT: D 94 GLU cc_start: 0.9005 (mp0) cc_final: 0.8757 (mp0) REVERT: D 96 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: D 100 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8265 (mpt90) REVERT: E 73 GLU cc_start: 0.8790 (tt0) cc_final: 0.8064 (tt0) REVERT: E 90 MET cc_start: 0.8661 (tpp) cc_final: 0.8136 (mmp) REVERT: F 22 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (mt) REVERT: F 25 ASN cc_start: 0.8491 (m110) cc_final: 0.7867 (m-40) REVERT: G 73 ASN cc_start: 0.8890 (t0) cc_final: 0.8498 (m-40) REVERT: G 75 LYS cc_start: 0.8734 (mttm) cc_final: 0.8510 (mmmm) REVERT: H 47 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (mptt) REVERT: H 52 ASP cc_start: 0.8407 (m-30) cc_final: 0.7865 (t0) REVERT: H 69 ASP cc_start: 0.8900 (t0) cc_final: 0.8585 (t0) REVERT: H 84 TYR cc_start: 0.8978 (m-10) cc_final: 0.8529 (m-10) REVERT: H 114 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8753 (mm-30) REVERT: K 84 GLU cc_start: 0.9176 (tp30) cc_final: 0.8859 (tp30) REVERT: K 87 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8698 (ttpp) REVERT: K 95 ASP cc_start: 0.8189 (t0) cc_final: 0.7683 (t0) REVERT: K 176 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8229 (tpt-90) REVERT: K 237 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7284 (tm-30) REVERT: K 239 ASP cc_start: 0.8773 (t0) cc_final: 0.8139 (t0) REVERT: N 95 ASP cc_start: 0.8189 (t0) cc_final: 0.7894 (t0) REVERT: N 108 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6833 (pp) REVERT: N 169 MET cc_start: 0.8826 (mmm) cc_final: 0.8454 (mmm) REVERT: N 263 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8746 (pm20) outliers start: 33 outliers final: 13 residues processed: 234 average time/residue: 0.6336 time to fit residues: 163.2988 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 81 optimal weight: 0.0770 chunk 144 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 73 ASN G 38 ASN G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.125522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077812 restraints weight = 38285.695| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.54 r_work: 0.2998 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17429 Z= 0.132 Angle : 0.640 13.590 24813 Z= 0.353 Chirality : 0.042 0.224 2799 Planarity : 0.005 0.104 2116 Dihedral : 29.755 169.651 4693 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.76 % Allowed : 30.16 % Favored : 67.08 % 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 (0.24), residues: 1306 helix: 2.53 (0.20), residues: 644 sheet: 0.19 (0.35), residues: 234 loop : -0.81 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG N 64 TYR 0.051 0.001 TYR D 84 PHE 0.006 0.001 PHE F 61 TRP 0.008 0.001 TRP K 199 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (17425) covalent geometry : angle 0.64034 / 0.35 (24805) SS BOND : bond 0.00294 / 0.17 ( 4) SS BOND : angle 0.73487 / 1.26 ( 8) hydrogen bonds : bond 0.03859 / 4.21 ( 950) hydrogen bonds : angle 3.41290 / 4.69 ( 2434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: L 197 MET cc_start: 0.3338 (mmm) cc_final: 0.2746 (mpt) REVERT: A 105 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: B 25 ASN cc_start: 0.8870 (m-40) cc_final: 0.8594 (m-40) REVERT: B 79 LYS cc_start: 0.9128 (mtmt) cc_final: 0.8821 (mtmt) REVERT: C 76 THR cc_start: 0.8991 (p) cc_final: 0.8617 (t) REVERT: D 69 ASP cc_start: 0.9125 (t0) cc_final: 0.8733 (t0) REVERT: D 87 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8172 (mmt-90) REVERT: D 94 GLU cc_start: 0.9028 (mp0) cc_final: 0.8818 (mp0) REVERT: E 73 GLU cc_start: 0.8779 (tt0) cc_final: 0.8013 (tt0) REVERT: E 90 MET cc_start: 0.8657 (tpp) cc_final: 0.8131 (mmp) REVERT: F 22 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (mt) REVERT: F 25 ASN cc_start: 0.8487 (m110) cc_final: 0.7839 (m-40) REVERT: G 73 ASN cc_start: 0.8890 (t0) cc_final: 0.8492 (m-40) REVERT: G 75 LYS cc_start: 0.8716 (mttm) cc_final: 0.8506 (mmmm) REVERT: H 47 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (mptt) REVERT: H 52 ASP cc_start: 0.8403 (m-30) cc_final: 0.7872 (t0) REVERT: H 69 ASP cc_start: 0.8908 (t0) cc_final: 0.8589 (t0) REVERT: H 84 TYR cc_start: 0.8976 (m-10) cc_final: 0.8529 (m-10) REVERT: H 114 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8794 (mm-30) REVERT: K 84 GLU cc_start: 0.9174 (tp30) cc_final: 0.8918 (tp30) REVERT: K 87 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8705 (ttpp) REVERT: K 95 ASP cc_start: 0.8187 (t0) cc_final: 0.7671 (t0) REVERT: K 103 MET cc_start: 0.9006 (ttt) cc_final: 0.8277 (ttp) REVERT: K 111 GLU cc_start: 0.9112 (pm20) cc_final: 0.8728 (pm20) REVERT: K 176 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8320 (tpt-90) REVERT: K 237 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7296 (tm-30) REVERT: K 239 ASP cc_start: 0.8778 (t0) cc_final: 0.8131 (t0) REVERT: N 95 ASP cc_start: 0.8167 (t0) cc_final: 0.7860 (t0) REVERT: N 108 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6609 (pp) REVERT: N 169 MET cc_start: 0.8848 (mmm) cc_final: 0.8501 (mmm) REVERT: N 177 VAL cc_start: 0.8500 (t) cc_final: 0.7993 (p) REVERT: N 263 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8760 (pm20) outliers start: 31 outliers final: 17 residues processed: 230 average time/residue: 0.5729 time to fit residues: 145.2307 Evaluate side-chains 225 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 0.0010 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN D 96 GLN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076558 restraints weight = 38130.772| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.84 r_work: 0.2974 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17429 Z= 0.160 Angle : 0.651 14.342 24813 Z= 0.359 Chirality : 0.043 0.212 2799 Planarity : 0.005 0.091 2116 Dihedral : 29.769 170.619 4693 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.20 % Allowed : 29.80 % Favored : 66.99 % 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: 1.54 (0.24), residues: 1306 helix: 2.51 (0.20), residues: 645 sheet: 0.16 (0.35), residues: 234 loop : -0.84 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 64 TYR 0.059 0.002 TYR D 84 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP K 199 HIS 0.005 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (17425) covalent geometry : angle 0.65102 / 0.36 (24805) SS BOND : bond 0.00347 / 0.22 ( 4) SS BOND : angle 0.78509 / 1.40 ( 8) hydrogen bonds : bond 0.03979 / 4.30 ( 950) hydrogen bonds : angle 3.40544 / 4.71 ( 2434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 197 MET cc_start: 0.3497 (mmm) cc_final: 0.2808 (mpt) REVERT: A 105 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: B 25 ASN cc_start: 0.8915 (m-40) cc_final: 0.8633 (m-40) REVERT: C 76 THR cc_start: 0.9035 (p) cc_final: 0.8689 (t) REVERT: D 69 ASP cc_start: 0.9131 (t0) cc_final: 0.8748 (t0) REVERT: D 94 GLU cc_start: 0.9021 (mp0) cc_final: 0.8762 (mp0) REVERT: E 73 GLU cc_start: 0.8816 (tt0) cc_final: 0.8100 (tt0) REVERT: E 90 MET cc_start: 0.8703 (tpp) cc_final: 0.8156 (mmp) REVERT: E 94 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8716 (mt-10) REVERT: F 25 ASN cc_start: 0.8466 (m110) cc_final: 0.7847 (m-40) REVERT: G 51 MET cc_start: 0.8901 (mmm) cc_final: 0.8634 (tpt) REVERT: G 73 ASN cc_start: 0.8913 (t0) cc_final: 0.8438 (m-40) REVERT: H 47 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8828 (mptt) REVERT: H 52 ASP cc_start: 0.8391 (m-30) cc_final: 0.7863 (t0) REVERT: H 69 ASP cc_start: 0.8984 (t0) cc_final: 0.8561 (t0) REVERT: H 84 TYR cc_start: 0.8990 (m-10) cc_final: 0.8523 (m-10) REVERT: H 114 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8772 (mm-30) REVERT: K 95 ASP cc_start: 0.8168 (t0) cc_final: 0.7672 (t0) REVERT: K 176 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8161 (tpt-90) REVERT: K 237 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7329 (tm-30) REVERT: K 239 ASP cc_start: 0.8790 (t0) cc_final: 0.8172 (t0) REVERT: N 95 ASP cc_start: 0.8189 (t0) cc_final: 0.7878 (t0) REVERT: N 108 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6838 (pp) REVERT: N 169 MET cc_start: 0.8834 (mmm) cc_final: 0.8524 (mmm) REVERT: N 177 VAL cc_start: 0.8589 (t) cc_final: 0.8114 (p) REVERT: N 263 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8742 (pm20) outliers start: 36 outliers final: 21 residues processed: 223 average time/residue: 0.6531 time to fit residues: 160.2459 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 182 LYS Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 7 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.124009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076712 restraints weight = 38616.951| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.61 r_work: 0.2972 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17429 Z= 0.163 Angle : 0.662 14.764 24813 Z= 0.364 Chirality : 0.043 0.212 2799 Planarity : 0.005 0.060 2116 Dihedral : 29.785 170.912 4693 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.49 % Allowed : 31.32 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1306 helix: 2.48 (0.20), residues: 645 sheet: 0.18 (0.35), residues: 228 loop : -0.81 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 71 TYR 0.056 0.002 TYR D 84 PHE 0.009 0.001 PHE F 61 TRP 0.010 0.001 TRP K 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (17425) covalent geometry : angle 0.66207 / 0.36 (24805) SS BOND : bond 0.00366 / 0.23 ( 4) SS BOND : angle 0.80149 / 1.43 ( 8) hydrogen bonds : bond 0.04035 / 4.40 ( 950) hydrogen bonds : angle 3.42726 / 4.74 ( 2434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: A 133 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 25 ASN cc_start: 0.8904 (m-40) cc_final: 0.8594 (m-40) REVERT: B 79 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8976 (mtmt) REVERT: C 76 THR cc_start: 0.9030 (p) cc_final: 0.8746 (t) REVERT: D 69 ASP cc_start: 0.9134 (t0) cc_final: 0.8796 (t0) REVERT: E 73 GLU cc_start: 0.8880 (tt0) cc_final: 0.8191 (tt0) REVERT: E 90 MET cc_start: 0.8670 (tpp) cc_final: 0.8148 (mmp) REVERT: E 94 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8716 (mt-10) REVERT: F 25 ASN cc_start: 0.8465 (m110) cc_final: 0.7884 (m-40) REVERT: G 51 MET cc_start: 0.8919 (mmm) cc_final: 0.8602 (tpt) REVERT: G 73 ASN cc_start: 0.8892 (t0) cc_final: 0.8547 (m-40) REVERT: G 91 GLU cc_start: 0.8272 (tt0) cc_final: 0.8053 (pt0) REVERT: H 47 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8865 (mptt) REVERT: H 52 ASP cc_start: 0.8367 (m-30) cc_final: 0.7861 (t0) REVERT: H 69 ASP cc_start: 0.8960 (t0) cc_final: 0.8570 (t0) REVERT: H 84 TYR cc_start: 0.9009 (m-10) cc_final: 0.8527 (m-10) REVERT: H 87 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8195 (mtp85) REVERT: H 114 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8778 (mm-30) REVERT: K 95 ASP cc_start: 0.8196 (t0) cc_final: 0.7730 (t0) REVERT: K 176 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8097 (tpt-90) REVERT: K 237 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7343 (tm-30) REVERT: K 239 ASP cc_start: 0.8761 (t0) cc_final: 0.8156 (t0) REVERT: N 95 ASP cc_start: 0.8164 (t0) cc_final: 0.7872 (t0) REVERT: N 108 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6960 (pp) REVERT: N 169 MET cc_start: 0.8879 (mmm) cc_final: 0.8636 (mmm) REVERT: N 177 VAL cc_start: 0.8702 (t) cc_final: 0.8267 (p) REVERT: N 214 ASP cc_start: 0.8571 (p0) cc_final: 0.8245 (p0) REVERT: N 263 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8794 (pm20) outliers start: 28 outliers final: 19 residues processed: 223 average time/residue: 0.6147 time to fit residues: 150.6996 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 65 GLN Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 38 ASN N 234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.124823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077381 restraints weight = 38419.084| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.59 r_work: 0.2993 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17429 Z= 0.138 Angle : 0.661 14.309 24813 Z= 0.361 Chirality : 0.042 0.210 2799 Planarity : 0.004 0.060 2116 Dihedral : 29.721 170.603 4693 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.14 % Allowed : 32.03 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1306 helix: 2.50 (0.20), residues: 644 sheet: 0.20 (0.35), residues: 228 loop : -0.87 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 71 TYR 0.037 0.001 TYR D 84 PHE 0.008 0.001 PHE F 61 TRP 0.010 0.001 TRP N 199 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (17425) covalent geometry : angle 0.66066 / 0.36 (24805) SS BOND : bond 0.00227 / 0.13 ( 4) SS BOND : angle 0.73560 / 1.32 ( 8) hydrogen bonds : bond 0.03853 / 4.25 ( 950) hydrogen bonds : angle 3.40755 / 4.71 ( 2434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6410.99 seconds wall clock time: 109 minutes 33.25 seconds (6573.25 seconds total)