Starting phenix.real_space_refine on Thu Aug 6 16:24:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sps_40683/08_2026/8sps_40683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sps_40683/08_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_40683/08_2026/8sps_40683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sps_40683/08_2026/8sps_40683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sps_40683/08_2026/8sps_40683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sps_40683/08_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-2.2rc3-6140/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: 3.10, per 1000 atoms: 0.19 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: 1.22 Conformation dependent library (CDL) restraints added in 461.3 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: 1.97 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: 2.90 Time building geometry restraints manager: 1.71 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: 0.960 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.860 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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= 0.645 Angle : 0.976 29.772 24813 Z= 0.703 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 0.97574 / 0.70 (24805) SS BOND : bond 0.00293 / 0.17 ( 4) SS BOND : angle 1.22539 / 2.21 ( 8) hydrogen bonds : bond 0.13037 / 14.18 ( 950) hydrogen bonds : angle 5.39350 / 7.18 ( 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 : 0.474 Fit side-chains 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: 0.7836 (m-40) REVERT: H 84 TYR cc_start: 0.8585 (m-10) cc_final: 0.8110 (m-10) outliers start: 6 outliers final: 2 residues processed: 362 average time/residue: 0.7171 time to fit residues: 284.0714 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 : 0.511 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.127543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081253 restraints weight = 38141.555| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.76 r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1964 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= 0.166 Angle : 0.706 8.922 24813 Z= 0.389 Chirality : 0.046 0.246 2799 Planarity : 0.006 0.080 2116 Dihedral : 29.896 172.070 4697 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.11 % Allowed : 26.60 % 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: 0.51 (0.22), residues: 1306 helix: 1.39 (0.19), residues: 647 sheet: -0.11 (0.33), residues: 234 loop : -0.97 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 219 TYR 0.023 0.001 TYR N 245 PHE 0.009 0.001 PHE N 256 TRP 0.010 0.001 TRP N 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (17425) covalent geometry : angle 0.70616 / 0.39 (24805) SS BOND : bond 0.00436 / 0.23 ( 4) SS BOND : angle 1.16572 / 1.96 ( 8) hydrogen bonds : bond 0.05041 / 5.43 ( 950) hydrogen bonds : angle 4.01201 / 5.45 ( 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 272 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: C 15 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8071 (ptpp) REVERT: C 91 GLU cc_start: 0.8588 (tt0) cc_final: 0.8265 (tt0) REVERT: D 69 ASP cc_start: 0.9115 (t0) cc_final: 0.8831 (t0) REVERT: D 87 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7863 (mmm-85) REVERT: D 94 GLU cc_start: 0.9059 (mp0) cc_final: 0.8818 (mp0) REVERT: D 114 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9090 (mm-30) REVERT: E 73 GLU cc_start: 0.8707 (tt0) cc_final: 0.8212 (tt0) REVERT: E 83 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6511 (ptm-80) REVERT: F 22 LEU cc_start: 0.8833 (mt) cc_final: 0.8570 (mt) REVERT: F 25 ASN cc_start: 0.8652 (m110) cc_final: 0.8155 (m-40) REVERT: F 95 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: G 20 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: G 73 ASN cc_start: 0.8675 (t0) cc_final: 0.8111 (m-40) REVERT: G 91 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: H 69 ASP cc_start: 0.8466 (t0) cc_final: 0.8225 (t0) REVERT: H 84 TYR cc_start: 0.8976 (m-10) cc_final: 0.8415 (m-10) REVERT: H 87 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8076 (mmm-85) REVERT: H 114 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8934 (mm-30) REVERT: K 32 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7727 (mm-30) REVERT: K 84 GLU cc_start: 0.9103 (tp30) cc_final: 0.8771 (tp30) REVERT: K 87 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8468 (ttpp) REVERT: K 95 ASP cc_start: 0.8030 (t0) cc_final: 0.7720 (t0) REVERT: K 111 GLU cc_start: 0.9340 (pm20) cc_final: 0.9052 (pm20) REVERT: K 176 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8360 (ttt90) REVERT: K 182 LYS cc_start: 0.8385 (tptt) cc_final: 0.8105 (tppt) REVERT: K 194 TYR cc_start: 0.8009 (m-80) cc_final: 0.7780 (m-80) REVERT: K 237 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7214 (tm-30) REVERT: N 103 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8150 (tpp) REVERT: N 239 ASP cc_start: 0.8067 (m-30) cc_final: 0.7836 (t0) outliers start: 35 outliers final: 14 residues processed: 258 average time/residue: 0.6287 time to fit residues: 178.3341 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 B residue 50 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL 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 K residue 59 VAL Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 103 MET 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: 5.9990 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: 3.9990 chunk 126 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 0.0050 overall best weight: 2.1600 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.124804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077638 restraints weight = 38562.344| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.73 r_work: 0.2987 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17429 Z= 0.191 Angle : 0.669 10.153 24813 Z= 0.371 Chirality : 0.045 0.215 2799 Planarity : 0.005 0.063 2116 Dihedral : 29.917 170.505 4693 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.27 % Allowed : 25.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1306 helix: 1.99 (0.20), residues: 645 sheet: -0.07 (0.34), residues: 234 loop : -0.91 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 20 TYR 0.026 0.002 TYR D 84 PHE 0.015 0.001 PHE N 256 TRP 0.010 0.001 TRP L 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17425) covalent geometry : angle 0.66886 / 0.37 (24805) SS BOND : bond 0.00490 / 0.23 ( 4) SS BOND : angle 0.90646 / 1.52 ( 8) hydrogen bonds : bond 0.04830 / 5.17 ( 950) hydrogen bonds : angle 3.73167 / 5.11 ( 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 268 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8951 (tppt) cc_final: 0.8745 (ttpp) REVERT: B 85 ASP cc_start: 0.8962 (m-30) cc_final: 0.8715 (m-30) REVERT: C 15 LYS cc_start: 0.8813 (mtpp) cc_final: 0.8604 (ptpp) REVERT: C 76 THR cc_start: 0.9072 (p) cc_final: 0.8675 (t) REVERT: C 91 GLU cc_start: 0.8600 (tt0) cc_final: 0.8238 (tt0) REVERT: D 87 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8165 (mmm-85) REVERT: D 94 GLU cc_start: 0.9058 (mp0) cc_final: 0.8852 (mp0) REVERT: D 100 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8712 (mpt-90) REVERT: D 114 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9058 (mm-30) REVERT: D 117 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9042 (ttpp) REVERT: E 73 GLU cc_start: 0.8638 (tt0) cc_final: 0.8037 (tt0) REVERT: F 25 ASN cc_start: 0.8563 (m110) cc_final: 0.7983 (m-40) REVERT: G 20 ARG cc_start: 0.8720 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: G 51 MET cc_start: 0.8914 (mmm) cc_final: 0.8673 (tpt) REVERT: G 73 ASN cc_start: 0.8736 (t0) cc_final: 0.8110 (m-40) REVERT: G 75 LYS cc_start: 0.8551 (mttm) cc_final: 0.8246 (mmmm) REVERT: G 92 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8063 (mt-10) REVERT: H 47 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8765 (mptp) REVERT: H 69 ASP cc_start: 0.8809 (t0) cc_final: 0.8482 (t0) REVERT: H 84 TYR cc_start: 0.9012 (m-10) cc_final: 0.8559 (m-10) REVERT: H 94 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: H 114 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8855 (mm-30) REVERT: K 32 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7839 (mm-30) REVERT: K 84 GLU cc_start: 0.9129 (tp30) cc_final: 0.8782 (tp30) REVERT: K 87 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8553 (ttpp) REVERT: K 95 ASP cc_start: 0.8071 (t0) cc_final: 0.7629 (t0) REVERT: K 103 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.7714 (tmm) REVERT: K 111 GLU cc_start: 0.9317 (pm20) cc_final: 0.9054 (pm20) REVERT: K 176 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8037 (tpt-90) REVERT: K 182 LYS cc_start: 0.8494 (tptt) cc_final: 0.8210 (tppt) REVERT: K 214 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8576 (m-30) REVERT: K 237 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7381 (tm-30) REVERT: N 64 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8858 (tpt90) REVERT: N 95 ASP cc_start: 0.8307 (t0) cc_final: 0.8081 (t0) REVERT: N 108 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7104 (pp) REVERT: N 263 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8820 (pm20) outliers start: 48 outliers final: 16 residues processed: 248 average time/residue: 0.7107 time to fit residues: 193.3343 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 50 ILE 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 D residue 117 LYS 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 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 94 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 170 HIS 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: 0.8980 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 125 GLN C 38 ASN C 73 ASN E 39 HIS 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 = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077588 restraints weight = 38321.121| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.55 r_work: 0.2995 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2692 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= 0.142 Angle : 0.642 10.415 24813 Z= 0.355 Chirality : 0.043 0.209 2799 Planarity : 0.004 0.056 2116 Dihedral : 29.841 168.983 4693 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 26.60 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1306 helix: 2.31 (0.20), residues: 643 sheet: 0.02 (0.34), residues: 234 loop : -0.89 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.048 0.001 TYR D 84 PHE 0.008 0.001 PHE N 256 TRP 0.010 0.001 TRP L 207 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (17425) covalent geometry : angle 0.64209 / 0.36 (24805) SS BOND : bond 0.00462 / 0.24 ( 4) SS BOND : angle 0.83989 / 1.39 ( 8) hydrogen bonds : bond 0.04239 / 4.58 ( 950) hydrogen bonds : angle 3.60303 / 4.96 ( 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 261 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 197 MET cc_start: 0.3317 (mmm) cc_final: 0.2732 (mpt) REVERT: A 133 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6893 (mt-10) REVERT: B 25 ASN cc_start: 0.8892 (m-40) cc_final: 0.8589 (m-40) REVERT: C 71 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8221 (ttp80) REVERT: C 76 THR cc_start: 0.9045 (p) cc_final: 0.8647 (t) REVERT: D 69 ASP cc_start: 0.9127 (t0) cc_final: 0.8774 (t0) REVERT: D 87 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8148 (mmm-85) REVERT: D 94 GLU cc_start: 0.9015 (mp0) cc_final: 0.8758 (mp0) REVERT: E 59 GLU cc_start: 0.8662 (pm20) cc_final: 0.8322 (pm20) REVERT: E 73 GLU cc_start: 0.8671 (tt0) cc_final: 0.8050 (tt0) REVERT: E 90 MET cc_start: 0.8685 (tpp) cc_final: 0.8196 (mmp) REVERT: E 123 ASP cc_start: 0.8556 (m-30) cc_final: 0.8126 (m-30) REVERT: F 23 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7744 (ptp-110) REVERT: F 25 ASN cc_start: 0.8573 (m110) cc_final: 0.7986 (m-40) REVERT: F 79 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8365 (tppp) REVERT: G 20 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.7848 (ttm110) REVERT: G 73 ASN cc_start: 0.8799 (t0) cc_final: 0.8342 (m-40) REVERT: G 75 LYS cc_start: 0.8571 (mttm) cc_final: 0.8297 (mmmm) REVERT: G 91 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: H 47 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8803 (mptm) REVERT: H 69 ASP cc_start: 0.8768 (t0) cc_final: 0.8497 (t0) REVERT: H 84 TYR cc_start: 0.8906 (m-10) cc_final: 0.8492 (m-10) REVERT: H 87 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7571 (mtm-85) REVERT: H 114 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8734 (mm-30) REVERT: K 32 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8110 (mm-30) REVERT: K 84 GLU cc_start: 0.9125 (tp30) cc_final: 0.8775 (tp30) REVERT: K 87 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8567 (ttpp) REVERT: K 95 ASP cc_start: 0.8159 (t0) cc_final: 0.7686 (t0) REVERT: K 111 GLU cc_start: 0.9308 (pm20) cc_final: 0.9069 (pm20) REVERT: K 176 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8250 (tpt-90) REVERT: K 182 LYS cc_start: 0.8563 (tptt) cc_final: 0.8301 (tppt) REVERT: N 95 ASP cc_start: 0.8303 (t0) cc_final: 0.8026 (t0) REVERT: N 103 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7875 (tpp) REVERT: N 108 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7142 (pp) REVERT: N 130 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8582 (p0) REVERT: N 169 MET cc_start: 0.8775 (mmm) cc_final: 0.8572 (mmp) outliers start: 43 outliers final: 18 residues processed: 245 average time/residue: 0.7245 time to fit residues: 194.5414 Evaluate side-chains 222 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain F residue 79 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 H residue 46 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 73 optimal weight: 0.0270 chunk 55 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 2 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.126235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078688 restraints weight = 38152.992| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.45 r_work: 0.3028 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2865 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= 0.127 Angle : 0.635 10.813 24813 Z= 0.352 Chirality : 0.042 0.210 2799 Planarity : 0.004 0.049 2116 Dihedral : 29.743 168.696 4693 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.83 % Allowed : 27.22 % Favored : 68.95 % 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: 1.48 (0.24), residues: 1306 helix: 2.43 (0.20), residues: 645 sheet: 0.10 (0.35), residues: 234 loop : -0.79 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.047 0.001 TYR D 84 PHE 0.007 0.001 PHE H 71 TRP 0.009 0.001 TRP L 207 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (17425) covalent geometry : angle 0.63540 / 0.35 (24805) SS BOND : bond 0.00325 / 0.16 ( 4) SS BOND : angle 0.74084 / 1.21 ( 8) hydrogen bonds : bond 0.04030 / 4.38 ( 950) hydrogen bonds : angle 3.50962 / 4.85 ( 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 269 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 197 MET cc_start: 0.3310 (mmm) cc_final: 0.2712 (mpt) REVERT: A 105 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: A 133 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: B 25 ASN cc_start: 0.8824 (m-40) cc_final: 0.8569 (m-40) REVERT: C 61 GLU cc_start: 0.8539 (tp30) cc_final: 0.8174 (tt0) REVERT: C 71 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8207 (ttp80) REVERT: C 76 THR cc_start: 0.8997 (p) cc_final: 0.8634 (t) REVERT: D 69 ASP cc_start: 0.9126 (t0) cc_final: 0.8766 (t0) REVERT: D 87 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: D 94 GLU cc_start: 0.8995 (mp0) cc_final: 0.8784 (mp0) REVERT: E 73 GLU cc_start: 0.8719 (tt0) cc_final: 0.7961 (tt0) REVERT: E 90 MET cc_start: 0.8671 (tpp) cc_final: 0.8244 (mmp) REVERT: E 123 ASP cc_start: 0.8567 (m-30) cc_final: 0.8159 (m-30) REVERT: F 22 LEU cc_start: 0.8778 (mt) cc_final: 0.8483 (mt) REVERT: F 25 ASN cc_start: 0.8492 (m110) cc_final: 0.7885 (m-40) REVERT: G 20 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.7818 (ttm110) REVERT: G 51 MET cc_start: 0.8933 (mmm) cc_final: 0.8655 (tpt) REVERT: G 73 ASN cc_start: 0.8829 (t0) cc_final: 0.8454 (m-40) REVERT: G 75 LYS cc_start: 0.8578 (mttm) cc_final: 0.8329 (mmmm) REVERT: H 41 TYR cc_start: 0.8432 (m-80) cc_final: 0.8230 (m-80) REVERT: H 47 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8743 (mptp) REVERT: H 52 ASP cc_start: 0.8384 (m-30) cc_final: 0.7849 (t0) REVERT: H 69 ASP cc_start: 0.8766 (t0) cc_final: 0.8484 (t0) REVERT: H 84 TYR cc_start: 0.8852 (m-10) cc_final: 0.8497 (m-10) REVERT: H 114 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8832 (mm-30) REVERT: K 32 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8205 (mm-30) REVERT: K 84 GLU cc_start: 0.9139 (tp30) cc_final: 0.8857 (tp30) REVERT: K 87 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8568 (ttpp) REVERT: K 95 ASP cc_start: 0.8184 (t0) cc_final: 0.7687 (t0) REVERT: K 103 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.7659 (tmm) REVERT: K 176 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8341 (tpt-90) REVERT: K 182 LYS cc_start: 0.8545 (tptt) cc_final: 0.8284 (tppt) REVERT: K 237 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7194 (tm-30) REVERT: K 239 ASP cc_start: 0.8686 (t0) cc_final: 0.8014 (t0) REVERT: N 95 ASP cc_start: 0.8237 (t0) cc_final: 0.7903 (t0) REVERT: N 108 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.6957 (pp) REVERT: N 112 ASP cc_start: 0.7926 (m-30) cc_final: 0.7724 (m-30) outliers start: 43 outliers final: 14 residues processed: 251 average time/residue: 0.7093 time to fit residues: 195.6541 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 D residue 39 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS 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 103 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 153 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 108 optimal weight: 0.0170 chunk 112 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 38 ASN C 73 ASN H 50 HIS N 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.125152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077484 restraints weight = 38590.870| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.53 r_work: 0.3001 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17429 Z= 0.149 Angle : 0.637 8.670 24813 Z= 0.354 Chirality : 0.043 0.216 2799 Planarity : 0.004 0.047 2116 Dihedral : 29.731 169.544 4693 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.02 % Allowed : 28.47 % Favored : 68.51 % 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: 0.12 (0.35), residues: 234 loop : -0.78 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 71 TYR 0.054 0.002 TYR D 84 PHE 0.007 0.001 PHE E 67 TRP 0.008 0.001 TRP L 207 HIS 0.004 0.001 HIS K 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (17425) covalent geometry : angle 0.63648 / 0.35 (24805) SS BOND : bond 0.00418 / 0.23 ( 4) SS BOND : angle 0.80613 / 1.39 ( 8) hydrogen bonds : bond 0.04086 / 4.43 ( 950) hydrogen bonds : angle 3.47628 / 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 242 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: L 197 MET cc_start: 0.3478 (mmm) cc_final: 0.3240 (mmt) REVERT: B 25 ASN cc_start: 0.8767 (m-40) cc_final: 0.8484 (m-40) REVERT: C 61 GLU cc_start: 0.8578 (tp30) cc_final: 0.8192 (tt0) REVERT: C 71 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8290 (ttp80) REVERT: C 76 THR cc_start: 0.9042 (p) cc_final: 0.8725 (t) REVERT: D 44 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: D 69 ASP cc_start: 0.9131 (t0) cc_final: 0.8786 (t0) REVERT: D 94 GLU cc_start: 0.8935 (mp0) cc_final: 0.8706 (mp0) REVERT: E 73 GLU cc_start: 0.8761 (tt0) cc_final: 0.8028 (tt0) REVERT: E 83 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6699 (ptm-80) REVERT: E 90 MET cc_start: 0.8632 (tpp) cc_final: 0.8108 (mmp) REVERT: E 123 ASP cc_start: 0.8618 (m-30) cc_final: 0.8238 (m-30) REVERT: F 22 LEU cc_start: 0.8825 (mt) cc_final: 0.8591 (mt) REVERT: F 23 ARG cc_start: 0.8232 (ptp-110) cc_final: 0.7852 (ptp-110) REVERT: F 25 ASN cc_start: 0.8506 (m110) cc_final: 0.7936 (m-40) REVERT: G 20 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8302 (ttp-110) REVERT: G 73 ASN cc_start: 0.8881 (t0) cc_final: 0.8525 (m-40) REVERT: G 75 LYS cc_start: 0.8736 (mttm) cc_final: 0.8511 (mmmm) REVERT: H 41 TYR cc_start: 0.8442 (m-80) cc_final: 0.8205 (m-80) REVERT: H 52 ASP cc_start: 0.8429 (m-30) cc_final: 0.7838 (t0) REVERT: H 69 ASP cc_start: 0.8821 (t0) cc_final: 0.8550 (t0) REVERT: H 84 TYR cc_start: 0.8871 (m-10) cc_final: 0.8520 (m-10) REVERT: H 114 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8813 (mm-30) REVERT: K 32 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8334 (mm-30) REVERT: K 84 GLU cc_start: 0.9126 (tp30) cc_final: 0.8820 (tp30) REVERT: K 87 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8687 (ttpp) REVERT: K 95 ASP cc_start: 0.8240 (t0) cc_final: 0.7757 (t0) REVERT: K 103 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.7666 (tmm) REVERT: K 169 MET cc_start: 0.7822 (pmm) cc_final: 0.7270 (pmm) REVERT: K 176 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8276 (tpt-90) REVERT: K 237 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7258 (tm-30) REVERT: K 239 ASP cc_start: 0.8757 (t0) cc_final: 0.8093 (t0) REVERT: N 95 ASP cc_start: 0.8276 (t0) cc_final: 0.7962 (t0) REVERT: N 108 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.6978 (pp) outliers start: 34 outliers final: 20 residues processed: 230 average time/residue: 0.6993 time to fit residues: 176.6246 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL 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 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 90 ASP 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 N residue 65 GLN Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 214 ASP 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: 2.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 38 ASN C 73 ASN N 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.124996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078001 restraints weight = 38225.263| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.48 r_work: 0.2999 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17429 Z= 0.147 Angle : 0.637 8.589 24813 Z= 0.355 Chirality : 0.043 0.216 2799 Planarity : 0.004 0.067 2116 Dihedral : 29.717 169.601 4693 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.29 % Allowed : 29.18 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1306 helix: 2.52 (0.20), residues: 645 sheet: 0.15 (0.35), residues: 234 loop : -0.76 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.061 0.001 TYR D 84 PHE 0.007 0.001 PHE F 61 TRP 0.008 0.001 TRP L 207 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (17425) covalent geometry : angle 0.63738 / 0.35 (24805) SS BOND : bond 0.00401 / 0.22 ( 4) SS BOND : angle 0.77216 / 1.31 ( 8) hydrogen bonds : bond 0.04017 / 4.36 ( 950) hydrogen bonds : angle 3.44254 / 4.74 ( 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 242 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7539 (tp30) REVERT: A 133 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: B 25 ASN cc_start: 0.8816 (m-40) cc_final: 0.8548 (m-40) REVERT: C 61 GLU cc_start: 0.8579 (tp30) cc_final: 0.8200 (tt0) REVERT: C 71 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8274 (ttp80) REVERT: C 72 ASP cc_start: 0.7801 (m-30) cc_final: 0.7559 (m-30) REVERT: C 76 THR cc_start: 0.9053 (p) cc_final: 0.8760 (t) REVERT: C 91 GLU cc_start: 0.8586 (tt0) cc_final: 0.8356 (tt0) REVERT: D 44 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8665 (mtmm) REVERT: D 69 ASP cc_start: 0.9131 (t0) cc_final: 0.8778 (t0) REVERT: D 87 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: D 94 GLU cc_start: 0.8960 (mp0) cc_final: 0.8612 (mp0) REVERT: E 59 GLU cc_start: 0.8756 (pm20) cc_final: 0.8518 (pm20) REVERT: E 73 GLU cc_start: 0.8773 (tt0) cc_final: 0.8029 (tt0) REVERT: E 80 THR cc_start: 0.8884 (m) cc_final: 0.8512 (m) REVERT: E 83 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.6803 (ptm-80) REVERT: E 90 MET cc_start: 0.8649 (tpp) cc_final: 0.8119 (mmp) REVERT: F 22 LEU cc_start: 0.8828 (mt) cc_final: 0.8558 (mt) REVERT: F 23 ARG cc_start: 0.8202 (ptp-110) cc_final: 0.7801 (ptp-110) REVERT: F 25 ASN cc_start: 0.8502 (m110) cc_final: 0.7918 (m-40) REVERT: G 20 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.7712 (ttm110) REVERT: G 51 MET cc_start: 0.8936 (mmm) cc_final: 0.8594 (tpt) REVERT: G 73 ASN cc_start: 0.8894 (t0) cc_final: 0.8527 (m-40) REVERT: G 75 LYS cc_start: 0.8750 (mttm) cc_final: 0.8525 (mmmm) REVERT: H 41 TYR cc_start: 0.8359 (m-80) cc_final: 0.8107 (m-80) REVERT: H 47 LYS cc_start: 0.9200 (tppt) cc_final: 0.8932 (mptm) REVERT: H 52 ASP cc_start: 0.8399 (m-30) cc_final: 0.7836 (t0) REVERT: H 69 ASP cc_start: 0.8856 (t0) cc_final: 0.8568 (t0) REVERT: H 84 TYR cc_start: 0.8922 (m-10) cc_final: 0.8558 (m-10) REVERT: H 87 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7637 (mtm-85) REVERT: H 114 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8780 (mm-30) REVERT: K 84 GLU cc_start: 0.9129 (tp30) cc_final: 0.8814 (tp30) REVERT: K 87 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8703 (ttpp) REVERT: K 95 ASP cc_start: 0.8226 (t0) cc_final: 0.7726 (t0) REVERT: K 103 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7705 (tmm) REVERT: K 111 GLU cc_start: 0.9150 (pm20) cc_final: 0.8770 (pm20) REVERT: K 169 MET cc_start: 0.7889 (pmm) cc_final: 0.7142 (pmm) REVERT: K 170 HIS cc_start: 0.8258 (m-70) cc_final: 0.8011 (m-70) REVERT: K 176 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8311 (tpt-90) REVERT: K 237 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7287 (tm-30) REVERT: K 239 ASP cc_start: 0.8779 (t0) cc_final: 0.8113 (t0) REVERT: N 95 ASP cc_start: 0.8281 (t0) cc_final: 0.7977 (t0) REVERT: N 108 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7026 (pp) REVERT: N 214 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8205 (p0) outliers start: 37 outliers final: 19 residues processed: 230 average time/residue: 0.7071 time to fit residues: 178.7344 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 A residue 112 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL 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 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 94 GLU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 38 ASN C 73 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078190 restraints weight = 38499.948| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.71 r_work: 0.3003 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17429 Z= 0.139 Angle : 0.650 12.257 24813 Z= 0.358 Chirality : 0.043 0.216 2799 Planarity : 0.004 0.056 2116 Dihedral : 29.679 169.747 4693 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.94 % Allowed : 29.36 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1306 helix: 2.52 (0.20), residues: 645 sheet: 0.57 (0.37), residues: 208 loop : -0.81 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 64 TYR 0.050 0.001 TYR D 84 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP K 199 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (17425) covalent geometry : angle 0.64995 / 0.36 (24805) SS BOND : bond 0.00357 / 0.21 ( 4) SS BOND : angle 0.76670 / 1.32 ( 8) hydrogen bonds : bond 0.03933 / 4.30 ( 950) hydrogen bonds : angle 3.40556 / 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: 33 poor density : 207 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: A 133 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: B 25 ASN cc_start: 0.8833 (m-40) cc_final: 0.8573 (m-40) REVERT: C 61 GLU cc_start: 0.8537 (tp30) cc_final: 0.8173 (tt0) REVERT: C 71 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8318 (ttp80) REVERT: C 72 ASP cc_start: 0.7845 (m-30) cc_final: 0.7617 (m-30) REVERT: C 76 THR cc_start: 0.9076 (p) cc_final: 0.8802 (t) REVERT: D 69 ASP cc_start: 0.9136 (t0) cc_final: 0.8787 (t0) REVERT: D 87 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8286 (mmm-85) REVERT: D 94 GLU cc_start: 0.8929 (mp0) cc_final: 0.8667 (mp0) REVERT: E 59 GLU cc_start: 0.8746 (pm20) cc_final: 0.8516 (pm20) REVERT: E 73 GLU cc_start: 0.8782 (tt0) cc_final: 0.8087 (tt0) REVERT: E 83 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.6871 (ptm-80) REVERT: E 90 MET cc_start: 0.8620 (tpp) cc_final: 0.8147 (mmp) REVERT: F 22 LEU cc_start: 0.8829 (mt) cc_final: 0.8544 (mt) REVERT: F 23 ARG cc_start: 0.8206 (ptp-110) cc_final: 0.7729 (ptp90) REVERT: F 25 ASN cc_start: 0.8470 (m110) cc_final: 0.7920 (m-40) REVERT: G 20 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.7815 (ttp-110) REVERT: G 73 ASN cc_start: 0.8920 (t0) cc_final: 0.8553 (m-40) REVERT: G 75 LYS cc_start: 0.8782 (mttm) cc_final: 0.8578 (mmmm) REVERT: H 41 TYR cc_start: 0.8321 (m-80) cc_final: 0.8064 (m-80) REVERT: H 47 LYS cc_start: 0.9209 (tppt) cc_final: 0.8960 (mptm) REVERT: H 52 ASP cc_start: 0.8307 (m-30) cc_final: 0.7797 (t0) REVERT: H 69 ASP cc_start: 0.8842 (t0) cc_final: 0.8559 (t0) REVERT: H 84 TYR cc_start: 0.8888 (m-10) cc_final: 0.8527 (m-10) REVERT: H 87 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7644 (mtm-85) REVERT: H 106 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7886 (tp30) REVERT: H 114 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8738 (mm-30) REVERT: K 84 GLU cc_start: 0.9152 (tp30) cc_final: 0.8890 (tp30) REVERT: K 87 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8736 (ttpp) REVERT: K 95 ASP cc_start: 0.8234 (t0) cc_final: 0.7735 (t0) REVERT: K 103 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: K 170 HIS cc_start: 0.8233 (m-70) cc_final: 0.8003 (m-70) REVERT: K 176 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8157 (tpt-90) REVERT: K 237 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7296 (tm-30) REVERT: K 239 ASP cc_start: 0.8780 (t0) cc_final: 0.8122 (t0) REVERT: N 95 ASP cc_start: 0.8240 (t0) cc_final: 0.7962 (t0) REVERT: N 108 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6886 (pp) outliers start: 33 outliers final: 16 residues processed: 229 average time/residue: 0.6617 time to fit residues: 166.6271 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain E residue 71 VAL 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 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN K 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.077883 restraints weight = 38470.090| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.89 r_work: 0.3008 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17429 Z= 0.136 Angle : 0.661 13.300 24813 Z= 0.362 Chirality : 0.042 0.217 2799 Planarity : 0.004 0.058 2116 Dihedral : 29.637 170.138 4693 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 29.54 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1306 helix: 2.54 (0.20), residues: 645 sheet: 0.20 (0.36), residues: 228 loop : -0.70 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 71 TYR 0.053 0.001 TYR D 84 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP K 199 HIS 0.004 0.001 HIS N 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17425) covalent geometry : angle 0.66071 / 0.36 (24805) SS BOND : bond 0.00294 / 0.17 ( 4) SS BOND : angle 0.75196 / 1.33 ( 8) hydrogen bonds : bond 0.03866 / 4.25 ( 950) hydrogen bonds : angle 3.37549 / 4.64 ( 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 256 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6040 (pt) cc_final: 0.5420 (pt) REVERT: L 197 MET cc_start: 0.3050 (mmm) cc_final: 0.2769 (mpt) REVERT: A 105 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7547 (tp30) REVERT: A 133 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: B 25 ASN cc_start: 0.8840 (m-40) cc_final: 0.8572 (m-40) REVERT: C 61 GLU cc_start: 0.8498 (tp30) cc_final: 0.8135 (tt0) REVERT: C 76 THR cc_start: 0.9092 (p) cc_final: 0.8832 (t) REVERT: D 69 ASP cc_start: 0.9148 (t0) cc_final: 0.8800 (t0) REVERT: D 87 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8335 (mmm-85) REVERT: D 94 GLU cc_start: 0.8932 (mp0) cc_final: 0.8666 (mp0) REVERT: E 59 GLU cc_start: 0.8787 (pm20) cc_final: 0.8529 (pm20) REVERT: E 73 GLU cc_start: 0.8809 (tt0) cc_final: 0.8096 (tt0) REVERT: E 83 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.6719 (ptm-80) REVERT: E 90 MET cc_start: 0.8628 (tpp) cc_final: 0.8150 (mmp) REVERT: F 22 LEU cc_start: 0.8829 (mt) cc_final: 0.8547 (mt) REVERT: F 23 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.7750 (ptp90) REVERT: F 25 ASN cc_start: 0.8472 (m110) cc_final: 0.7913 (m-40) REVERT: G 20 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.7730 (ttp-110) REVERT: G 73 ASN cc_start: 0.8925 (t0) cc_final: 0.8553 (m-40) REVERT: H 41 TYR cc_start: 0.8308 (m-80) cc_final: 0.8074 (m-80) REVERT: H 47 LYS cc_start: 0.9127 (tppt) cc_final: 0.8897 (mptm) REVERT: H 52 ASP cc_start: 0.8277 (m-30) cc_final: 0.7792 (t0) REVERT: H 69 ASP cc_start: 0.8847 (t0) cc_final: 0.8569 (t0) REVERT: H 84 TYR cc_start: 0.8903 (m-10) cc_final: 0.8541 (m-10) REVERT: H 87 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7829 (mtm-85) REVERT: H 114 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8727 (mm-30) REVERT: K 23 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6745 (tp30) REVERT: K 84 GLU cc_start: 0.9155 (tp30) cc_final: 0.8858 (tp30) REVERT: K 87 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8727 (ttpp) REVERT: K 95 ASP cc_start: 0.8226 (t0) cc_final: 0.7735 (t0) REVERT: K 169 MET cc_start: 0.8019 (pmm) cc_final: 0.7769 (pmm) REVERT: K 176 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8088 (tpt-90) REVERT: K 237 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7729 (tm-30) REVERT: K 239 ASP cc_start: 0.8778 (t0) cc_final: 0.8569 (t0) REVERT: N 95 ASP cc_start: 0.8221 (t0) cc_final: 0.7931 (t0) outliers start: 32 outliers final: 19 residues processed: 242 average time/residue: 0.6802 time to fit residues: 181.0565 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 A residue 133 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 D residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL 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 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 94 GLU 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 170 HIS 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: 6.9990 chunk 124 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.123331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075914 restraints weight = 38597.230| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.52 r_work: 0.2954 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17429 Z= 0.204 Angle : 0.707 10.334 24813 Z= 0.383 Chirality : 0.045 0.223 2799 Planarity : 0.005 0.053 2116 Dihedral : 29.729 171.666 4693 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.40 % Allowed : 30.96 % Favored : 66.64 % 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: 1.40 (0.24), residues: 1306 helix: 2.42 (0.20), residues: 642 sheet: 0.07 (0.35), residues: 232 loop : -0.89 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 71 TYR 0.022 0.002 TYR B 88 PHE 0.010 0.001 PHE A 104 TRP 0.010 0.001 TRP N 199 HIS 0.008 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (17425) covalent geometry : angle 0.70684 / 0.38 (24805) SS BOND : bond 0.00536 / 0.35 ( 4) SS BOND : angle 0.84241 / 1.58 ( 8) hydrogen bonds : bond 0.04438 / 4.84 ( 950) hydrogen bonds : angle 3.52414 / 4.81 ( 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 230 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6138 (pt) cc_final: 0.5562 (pt) REVERT: L 197 MET cc_start: 0.2883 (mmm) cc_final: 0.2496 (mpt) REVERT: A 105 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: A 133 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: B 25 ASN cc_start: 0.8914 (m-40) cc_final: 0.8673 (m-40) REVERT: C 61 GLU cc_start: 0.8545 (tp30) cc_final: 0.8183 (tt0) REVERT: C 76 THR cc_start: 0.9124 (p) cc_final: 0.8873 (t) REVERT: D 87 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: D 94 GLU cc_start: 0.8970 (mp0) cc_final: 0.8670 (mp0) REVERT: E 59 GLU cc_start: 0.8811 (pm20) cc_final: 0.8570 (pm20) REVERT: E 73 GLU cc_start: 0.8830 (tt0) cc_final: 0.8070 (tt0) REVERT: E 83 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6665 (ptm-80) REVERT: E 90 MET cc_start: 0.8709 (tpp) cc_final: 0.8209 (mmp) REVERT: F 22 LEU cc_start: 0.8903 (mt) cc_final: 0.8672 (mt) REVERT: F 23 ARG cc_start: 0.8268 (ptp-110) cc_final: 0.7806 (ptp90) REVERT: F 25 ASN cc_start: 0.8471 (m110) cc_final: 0.7879 (m-40) REVERT: G 20 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.7761 (ttp-110) REVERT: G 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8573 (m-40) REVERT: H 41 TYR cc_start: 0.8418 (m-80) cc_final: 0.8192 (m-80) REVERT: H 47 LYS cc_start: 0.9149 (tppt) cc_final: 0.8938 (mptm) REVERT: H 52 ASP cc_start: 0.8367 (m-30) cc_final: 0.7830 (t0) REVERT: H 69 ASP cc_start: 0.8997 (t0) cc_final: 0.8681 (t0) REVERT: H 84 TYR cc_start: 0.8968 (m-10) cc_final: 0.8596 (m-10) REVERT: H 114 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8801 (mm-30) REVERT: K 95 ASP cc_start: 0.8147 (t0) cc_final: 0.7667 (t0) REVERT: K 169 MET cc_start: 0.8128 (pmm) cc_final: 0.7675 (pmm) REVERT: K 176 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8120 (tpt-90) REVERT: K 237 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7799 (tm-30) REVERT: K 239 ASP cc_start: 0.8803 (t0) cc_final: 0.8578 (t0) REVERT: N 95 ASP cc_start: 0.8216 (t0) cc_final: 0.7905 (t0) REVERT: N 108 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7059 (pp) REVERT: N 214 ASP cc_start: 0.8617 (p0) cc_final: 0.8306 (p0) outliers start: 27 outliers final: 19 residues processed: 224 average time/residue: 0.6595 time to fit residues: 162.1543 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL 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 96 THR Chi-restraints excluded: chain G residue 90 ASP 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 137 SER Chi-restraints excluded: chain K residue 182 LYS Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 111 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078475 restraints weight = 38267.501| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.61 r_work: 0.2991 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3636 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= 0.141 Angle : 0.675 14.450 24813 Z= 0.367 Chirality : 0.043 0.217 2799 Planarity : 0.004 0.052 2116 Dihedral : 29.659 170.476 4693 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.31 % Allowed : 31.41 % Favored : 66.28 % 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: 1.43 (0.24), residues: 1306 helix: 2.45 (0.20), residues: 644 sheet: 0.12 (0.35), residues: 232 loop : -0.93 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 64 TYR 0.018 0.001 TYR G 57 PHE 0.007 0.001 PHE F 61 TRP 0.012 0.001 TRP N 58 HIS 0.007 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (17425) covalent geometry : angle 0.67466 / 0.37 (24805) SS BOND : bond 0.00334 / 0.19 ( 4) SS BOND : angle 0.82017 / 1.56 ( 8) hydrogen bonds : bond 0.03944 / 4.38 ( 950) hydrogen bonds : angle 3.43602 / 4.71 ( 2434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7175.13 seconds wall clock time: 122 minutes 33.12 seconds (7353.12 seconds total)