Starting phenix.real_space_refine on Fri Jul 3 19:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.map" model { file = "/net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spu_40686/07_2026/8spu_40686.cif" } resolution = 2.8 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= 0.054 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 298 5.49 5 S 35 5.16 5 C 9259 2.51 5 N 2928 2.21 5 O 3661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16181 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3011 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "I" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3098 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "L" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 559 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" 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: "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: "A" 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: "B" 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: "C" 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: "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: "N" 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: "K" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 3.03, per 1000 atoms: 0.19 Number of scatterers: 16181 At special positions: 0 Unit cell: (128.832, 121.44, 134.112, 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 35 16.00 P 298 15.00 O 3661 8.00 N 2928 7.00 C 9259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 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 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: 1.02 Conformation dependent library (CDL) restraints added in 385.9 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 49.5% alpha, 18.6% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'L' and resid 140 through 161 Processing helix chain 'L' and resid 163 through 176 removed outlier: 3.952A pdb=" N GLY L 172 " --> pdb=" O GLY L 168 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 190 Processing helix chain 'L' and resid 193 through 214 Proline residue: L 202 - end of helix removed outlier: 3.555A pdb=" N GLU L 209 " --> pdb=" O GLN L 205 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.646A pdb=" N LEU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.549A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.511A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.620A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 4.115A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) 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 84 through 87 removed outlier: 3.828A pdb=" N LYS K 87 " --> pdb=" O GLU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 84 through 87' Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.673A pdb=" N ASP K 112 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 109 through 113' Processing helix chain 'K' and resid 237 through 241 removed outlier: 3.709A pdb=" N ASP K 240 " --> pdb=" O GLU K 237 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR K 241 " --> pdb=" O SER K 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.573A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.153A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.139A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'N' and resid 25 through 28 removed outlier: 3.563A pdb=" N VAL N 101 " --> pdb=" O CYS N 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR N 54 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR N 74 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET N 169 " --> pdb=" O LYS N 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 168 through 171 removed outlier: 3.502A pdb=" N MET N 169 " --> pdb=" O LYS N 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU N 263 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA N 171 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR N 255 " --> pdb=" O GLN N 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'K' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS K 60 " --> pdb=" O TRP K 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP K 69 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR K 62 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU K 67 " --> pdb=" O THR K 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR K 131 " --> pdb=" O ARG K 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'K' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE K 229 " --> pdb=" O CYS K 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 228 " --> pdb=" O SER K 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 168 through 171 removed outlier: 6.817A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 1.38 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: 4743 1.36 - 1.51: 7218 1.51 - 1.67: 5065 1.67 - 1.83: 55 Bond restraints: 17096 Sorted by residual: bond pdb=" C LEU F 90 " pdb=" O LEU F 90 " ideal model delta sigma weight residual 1.237 1.053 0.184 1.19e-02 7.06e+03 2.39e+02 bond pdb=" C MET G 51 " pdb=" O MET G 51 " ideal model delta sigma weight residual 1.236 1.044 0.192 1.29e-02 6.01e+03 2.22e+02 bond pdb=" C LEU G 93 " pdb=" O LEU G 93 " ideal model delta sigma weight residual 1.237 1.070 0.167 1.17e-02 7.31e+03 2.04e+02 bond pdb=" C ASN G 94 " pdb=" O ASN G 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.64e+02 bond pdb=" CA MET G 51 " pdb=" C MET G 51 " ideal model delta sigma weight residual 1.523 1.362 0.161 1.37e-02 5.33e+03 1.38e+02 ... (remaining 17091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.96: 24319 5.96 - 11.91: 54 11.91 - 17.87: 11 17.87 - 23.82: 2 23.82 - 29.78: 1 Bond angle restraints: 24387 Sorted by residual: angle pdb=" N SER D 33 " pdb=" CA SER D 33 " pdb=" C SER D 33 " ideal model delta sigma weight residual 110.61 126.86 -16.25 1.25e+00 6.40e-01 1.69e+02 angle pdb=" CB MET G 51 " pdb=" CG MET G 51 " pdb=" SD MET G 51 " ideal model delta sigma weight residual 112.70 82.92 29.78 3.00e+00 1.11e-01 9.85e+01 angle pdb=" N LYS G 13 " pdb=" CA LYS G 13 " pdb=" C LYS G 13 " ideal model delta sigma weight residual 110.80 128.75 -17.95 2.13e+00 2.20e-01 7.10e+01 angle pdb=" C LYS G 13 " pdb=" N ALA G 14 " pdb=" CA ALA G 14 " ideal model delta sigma weight residual 121.54 134.10 -12.56 1.91e+00 2.74e-01 4.33e+01 angle pdb=" CA GLN F 93 " pdb=" CB GLN F 93 " pdb=" CG GLN F 93 " ideal model delta sigma weight residual 114.10 101.76 12.34 2.00e+00 2.50e-01 3.81e+01 ... (remaining 24382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 7841 34.97 - 69.95: 1631 69.95 - 104.92: 28 104.92 - 139.89: 3 139.89 - 174.87: 3 Dihedral angle restraints: 9506 sinusoidal: 5777 harmonic: 3729 Sorted by residual: dihedral pdb=" C LEU A 82 " pdb=" N LEU A 82 " pdb=" CA LEU A 82 " pdb=" CB LEU A 82 " ideal model delta harmonic sigma weight residual -122.60 -108.43 -14.17 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" C SER D 33 " pdb=" N SER D 33 " pdb=" CA SER D 33 " pdb=" CB SER D 33 " ideal model delta harmonic sigma weight residual -122.60 -134.47 11.87 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2716 0.137 - 0.274: 31 0.274 - 0.410: 6 0.410 - 0.547: 2 0.547 - 0.684: 2 Chirality restraints: 2757 Sorted by residual: chirality pdb=" CA SER D 33 " pdb=" N SER D 33 " pdb=" C SER D 33 " pdb=" CB SER D 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 G 93 " pdb=" CB LEU G 93 " pdb=" CD1 LEU G 93 " pdb=" CD2 LEU G 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS G 13 " pdb=" N LYS G 13 " pdb=" C LYS G 13 " pdb=" CB LYS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 2754 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 92 " 0.035 2.00e-02 2.50e+03 7.35e-02 5.40e+01 pdb=" C GLU G 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU G 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU G 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 51 " 0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET G 51 " -0.092 2.00e-02 2.50e+03 pdb=" O MET G 51 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA G 52 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR K 62 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO K 63 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO K 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO K 63 " 0.067 5.00e-02 4.00e+02 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 40 2.48 - 3.08: 9878 3.08 - 3.69: 27048 3.69 - 4.29: 41559 4.29 - 4.90: 61617 Nonbonded interactions: 140142 Sorted by model distance: nonbonded pdb=" C7 DT J 11 " pdb=" NH2 ARG L 186 " model vdw 1.874 3.540 nonbonded pdb=" O SER D 33 " pdb=" OG SER D 33 " model vdw 2.087 3.040 nonbonded pdb=" CG LYS G 13 " pdb=" N ALA G 14 " model vdw 2.181 3.520 nonbonded pdb=" OP1 DG I 163 " pdb=" NH1 ARG A 42 " model vdw 2.247 3.120 nonbonded pdb=" O GLN L 155 " pdb=" OG1 THR L 159 " model vdw 2.254 3.040 ... (remaining 140137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = (chain 'K' 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 )))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 0.192 17100 Z= 0.653 Angle : 0.997 29.775 24395 Z= 0.708 Chirality : 0.056 0.684 2757 Planarity : 0.007 0.127 2046 Dihedral : 27.152 174.865 7102 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 0.47 % Allowed : 21.88 % Favored : 77.65 % Cbeta Deviations : 0.25 % 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: -0.88 (0.21), residues: 1259 helix: -0.12 (0.18), residues: 603 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 100 TYR 0.046 0.002 TYR D 41 PHE 0.029 0.003 PHE E 78 TRP 0.010 0.002 TRP K 58 HIS 0.006 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00890 / 0.65 (17096) covalent geometry : angle 0.99701 / 0.71 (24387) SS BOND : bond 0.00315 / 0.18 ( 4) SS BOND : angle 1.24302 / 1.80 ( 8) hydrogen bonds : bond 0.12129 / 12.00 ( 943) hydrogen bonds : angle 5.40658 / 6.66 ( 2398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 120 MET cc_start: 0.8446 (mmm) cc_final: 0.8198 (mpp) REVERT: G 51 MET cc_start: 0.8050 (tpt) cc_final: 0.7798 (tpp) REVERT: G 91 GLU cc_start: 0.8050 (tp30) cc_final: 0.7826 (tp30) REVERT: C 73 ASN cc_start: 0.8266 (t0) cc_final: 0.7985 (t0) REVERT: D 69 ASP cc_start: 0.8106 (t70) cc_final: 0.7833 (t0) REVERT: D 72 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7296 (mt-10) REVERT: N 130 ASP cc_start: 0.8258 (p0) cc_final: 0.8032 (p0) REVERT: K 42 MET cc_start: 0.8231 (mtm) cc_final: 0.8022 (mtp) REVERT: K 103 MET cc_start: 0.8178 (ttt) cc_final: 0.7795 (ttt) REVERT: K 235 ASN cc_start: 0.7834 (p0) cc_final: 0.7433 (p0) outliers start: 5 outliers final: 1 residues processed: 332 average time/residue: 0.8535 time to fit residues: 304.7338 Evaluate side-chains 223 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 164 GLN E 39 HIS G 31 HIS H 64 ASN H 85 ASN B 64 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 164 GLN K 134 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067325 restraints weight = 33228.806| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.74 r_work: 0.2860 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17100 Z= 0.158 Angle : 0.686 16.826 24395 Z= 0.381 Chirality : 0.045 0.298 2757 Planarity : 0.005 0.067 2046 Dihedral : 29.949 175.142 4686 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.63 % Allowed : 25.70 % Favored : 70.67 % 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: 0.59 (0.23), residues: 1259 helix: 1.44 (0.20), residues: 608 sheet: 0.07 (0.34), residues: 232 loop : -0.91 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 87 TYR 0.014 0.001 TYR C 50 PHE 0.012 0.001 PHE L 149 TRP 0.010 0.001 TRP N 199 HIS 0.006 0.001 HIS K 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (17096) covalent geometry : angle 0.68590 / 0.38 (24387) SS BOND : bond 0.00421 / 0.28 ( 4) SS BOND : angle 1.07158 / 1.36 ( 8) hydrogen bonds : bond 0.04627 / 5.03 ( 943) hydrogen bonds : angle 3.89286 / 4.82 ( 2398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: F 25 ASN cc_start: 0.9221 (m-40) cc_final: 0.8607 (m-40) REVERT: F 79 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8524 (mtmm) REVERT: G 13 LYS cc_start: 0.7293 (tptt) cc_final: 0.6534 (mppt) REVERT: G 41 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7944 (tm-30) REVERT: H 36 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: H 72 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: A 90 MET cc_start: 0.8961 (mtm) cc_final: 0.8745 (mtp) REVERT: A 99 TYR cc_start: 0.9514 (t80) cc_final: 0.9168 (t80) REVERT: A 133 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: B 24 ASP cc_start: 0.7690 (p0) cc_final: 0.7143 (p0) REVERT: C 73 ASN cc_start: 0.8381 (t0) cc_final: 0.8144 (t160) REVERT: C 91 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: D 69 ASP cc_start: 0.8949 (t70) cc_final: 0.8622 (t0) REVERT: D 72 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8537 (mt-10) REVERT: N 240 ASP cc_start: 0.8937 (m-30) cc_final: 0.8432 (m-30) REVERT: K 42 MET cc_start: 0.8563 (mtm) cc_final: 0.8332 (mtp) REVERT: K 64 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8365 (ttp80) REVERT: K 103 MET cc_start: 0.8547 (ttt) cc_final: 0.7985 (ttt) REVERT: K 219 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7869 (mtm110) REVERT: K 235 ASN cc_start: 0.8143 (p0) cc_final: 0.7235 (p0) REVERT: K 237 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7122 (mp0) outliers start: 39 outliers final: 13 residues processed: 264 average time/residue: 0.7544 time to fit residues: 216.4823 Evaluate side-chains 242 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 137 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062267 restraints weight = 33430.211| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.69 r_work: 0.2747 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17100 Z= 0.254 Angle : 0.700 13.053 24395 Z= 0.386 Chirality : 0.047 0.282 2757 Planarity : 0.005 0.060 2046 Dihedral : 30.160 166.753 4685 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.00 % Allowed : 25.14 % Favored : 70.86 % 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: 1.08 (0.24), residues: 1259 helix: 2.06 (0.21), residues: 607 sheet: 0.18 (0.35), residues: 224 loop : -0.95 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 87 TYR 0.016 0.002 TYR C 50 PHE 0.014 0.002 PHE H 71 TRP 0.011 0.002 TRP K 58 HIS 0.007 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (17096) covalent geometry : angle 0.69933 / 0.39 (24387) SS BOND : bond 0.00566 / 0.38 ( 4) SS BOND : angle 1.13036 / 1.65 ( 8) hydrogen bonds : bond 0.05327 / 5.61 ( 943) hydrogen bonds : angle 3.72435 / 4.60 ( 2398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8541 (pm20) cc_final: 0.8225 (pm20) REVERT: F 79 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8587 (mtmm) REVERT: F 84 MET cc_start: 0.9135 (mmm) cc_final: 0.8842 (mmm) REVERT: G 41 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7907 (tm-30) REVERT: G 64 GLU cc_start: 0.9048 (tt0) cc_final: 0.8808 (tt0) REVERT: G 92 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8711 (mt-10) REVERT: H 72 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8502 (tm-30) REVERT: H 114 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8839 (mm-30) REVERT: A 56 LYS cc_start: 0.9390 (ptmm) cc_final: 0.9023 (ptpp) REVERT: A 133 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 77 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9097 (mmtp) REVERT: B 92 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8721 (ttp80) REVERT: B 95 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7683 (mtp180) REVERT: C 36 LYS cc_start: 0.9171 (mmpt) cc_final: 0.8923 (mmpt) REVERT: C 73 ASN cc_start: 0.8607 (t0) cc_final: 0.8274 (t160) REVERT: C 91 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: C 104 GLN cc_start: 0.9115 (mm110) cc_final: 0.8903 (mm110) REVERT: D 72 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8603 (mt-10) REVERT: N 27 GLN cc_start: 0.8892 (tp40) cc_final: 0.8664 (tp-100) REVERT: N 64 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8225 (tmm-80) REVERT: N 65 GLN cc_start: 0.8794 (mp10) cc_final: 0.8466 (mp10) REVERT: N 95 ASP cc_start: 0.8326 (t0) cc_final: 0.8083 (t0) REVERT: N 237 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8112 (mp0) REVERT: K 42 MET cc_start: 0.8809 (mtm) cc_final: 0.8489 (mtp) REVERT: K 95 ASP cc_start: 0.8936 (t0) cc_final: 0.8736 (t0) REVERT: K 103 MET cc_start: 0.8748 (ttt) cc_final: 0.8188 (ttt) REVERT: K 111 GLU cc_start: 0.8840 (pp20) cc_final: 0.8284 (pp20) REVERT: K 112 ASP cc_start: 0.8456 (m-30) cc_final: 0.8180 (m-30) REVERT: K 139 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8868 (p) REVERT: K 264 ILE cc_start: 0.8892 (mm) cc_final: 0.8507 (mm) outliers start: 43 outliers final: 16 residues processed: 252 average time/residue: 0.7992 time to fit residues: 217.3416 Evaluate side-chains 227 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 26 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 40.0000 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN N 25 GLN N 134 GLN N 164 GLN N 235 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061436 restraints weight = 33148.000| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.61 r_work: 0.2720 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17100 Z= 0.246 Angle : 0.682 11.777 24395 Z= 0.376 Chirality : 0.046 0.287 2757 Planarity : 0.004 0.044 2046 Dihedral : 30.232 167.562 4685 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 4.28 % Allowed : 25.14 % Favored : 70.58 % 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: 1.23 (0.24), residues: 1259 helix: 2.22 (0.21), residues: 609 sheet: 0.22 (0.35), residues: 224 loop : -0.95 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 64 TYR 0.014 0.002 TYR C 50 PHE 0.010 0.002 PHE L 149 TRP 0.009 0.002 TRP N 69 HIS 0.005 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.25 (17096) covalent geometry : angle 0.68179 / 0.38 (24387) SS BOND : bond 0.00603 / 0.44 ( 4) SS BOND : angle 0.99760 / 1.36 ( 8) hydrogen bonds : bond 0.04702 / 4.99 ( 943) hydrogen bonds : angle 3.64313 / 4.54 ( 2398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8551 (pm20) cc_final: 0.8246 (pm20) REVERT: F 79 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8570 (mtmm) REVERT: G 41 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7870 (tm-30) REVERT: G 64 GLU cc_start: 0.9080 (tt0) cc_final: 0.8844 (tt0) REVERT: A 56 LYS cc_start: 0.9401 (ptmm) cc_final: 0.9068 (ptpp) REVERT: A 99 TYR cc_start: 0.9538 (t80) cc_final: 0.9236 (t80) REVERT: A 133 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 77 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8955 (mmtp) REVERT: B 92 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8615 (ttp80) REVERT: B 95 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7475 (mtp180) REVERT: C 73 ASN cc_start: 0.8639 (t0) cc_final: 0.8285 (t160) REVERT: C 91 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: D 69 ASP cc_start: 0.9258 (t70) cc_final: 0.8894 (t0) REVERT: D 72 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8652 (mt-10) REVERT: N 64 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8240 (tmm-80) REVERT: N 65 GLN cc_start: 0.8670 (mp10) cc_final: 0.8424 (mp10) REVERT: N 95 ASP cc_start: 0.8366 (t0) cc_final: 0.8032 (t0) REVERT: N 134 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: N 200 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8541 (mppt) REVERT: K 42 MET cc_start: 0.8858 (mtm) cc_final: 0.8524 (mtp) REVERT: K 45 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8941 (tmtm) REVERT: K 95 ASP cc_start: 0.8876 (t0) cc_final: 0.8608 (t0) REVERT: K 103 MET cc_start: 0.8800 (ttt) cc_final: 0.8257 (ttt) outliers start: 46 outliers final: 19 residues processed: 235 average time/residue: 0.7904 time to fit residues: 200.7417 Evaluate side-chains 224 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 134 GLN Chi-restraints excluded: chain N residue 200 LYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 14 optimal weight: 50.0000 chunk 139 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 30.0000 chunk 64 optimal weight: 0.6980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN A 68 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.104699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061100 restraints weight = 33261.400| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.75 r_work: 0.2729 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17100 Z= 0.214 Angle : 0.654 11.559 24395 Z= 0.362 Chirality : 0.045 0.286 2757 Planarity : 0.004 0.041 2046 Dihedral : 30.207 166.584 4685 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.10 % Allowed : 25.14 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1259 helix: 2.37 (0.21), residues: 611 sheet: 0.56 (0.34), residues: 236 loop : -0.89 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.014 0.001 TYR K 72 PHE 0.009 0.001 PHE L 149 TRP 0.007 0.001 TRP K 58 HIS 0.004 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (17096) covalent geometry : angle 0.65399 / 0.36 (24387) SS BOND : bond 0.00480 / 0.32 ( 4) SS BOND : angle 0.97355 / 1.26 ( 8) hydrogen bonds : bond 0.04567 / 4.84 ( 943) hydrogen bonds : angle 3.57884 / 4.48 ( 2398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8612 (pm20) cc_final: 0.8328 (pm20) REVERT: F 79 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: F 91 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8996 (ttmt) REVERT: G 41 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7883 (tm-30) REVERT: G 64 GLU cc_start: 0.9087 (tt0) cc_final: 0.8855 (tt0) REVERT: A 56 LYS cc_start: 0.9389 (ptmm) cc_final: 0.9070 (ptpp) REVERT: A 81 ASP cc_start: 0.8843 (m-30) cc_final: 0.8641 (p0) REVERT: A 99 TYR cc_start: 0.9544 (t80) cc_final: 0.9247 (t80) REVERT: A 133 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7831 (mt-10) REVERT: B 77 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8974 (mmtp) REVERT: B 92 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8544 (ttp80) REVERT: B 95 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7524 (mtp180) REVERT: C 73 ASN cc_start: 0.8648 (t0) cc_final: 0.8284 (t160) REVERT: C 91 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: C 95 LYS cc_start: 0.9175 (tmtm) cc_final: 0.8943 (ttmt) REVERT: D 69 ASP cc_start: 0.9269 (t70) cc_final: 0.8861 (t0) REVERT: N 23 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: N 64 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8370 (ttp80) REVERT: N 95 ASP cc_start: 0.8450 (t0) cc_final: 0.8048 (t0) REVERT: N 176 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: K 42 MET cc_start: 0.8897 (mtm) cc_final: 0.8557 (mtp) REVERT: K 45 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8966 (tmtm) REVERT: K 64 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8404 (ttp80) REVERT: K 95 ASP cc_start: 0.8963 (t0) cc_final: 0.8720 (t0) REVERT: K 139 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8927 (p) outliers start: 44 outliers final: 16 residues processed: 238 average time/residue: 0.7976 time to fit residues: 205.3612 Evaluate side-chains 225 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.106603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063449 restraints weight = 33093.671| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.61 r_work: 0.2765 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17100 Z= 0.135 Angle : 0.613 11.612 24395 Z= 0.345 Chirality : 0.042 0.293 2757 Planarity : 0.004 0.039 2046 Dihedral : 30.025 167.015 4685 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.82 % Allowed : 25.70 % Favored : 70.48 % 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: 1.73 (0.24), residues: 1259 helix: 2.60 (0.21), residues: 612 sheet: 0.55 (0.34), residues: 236 loop : -0.77 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.014 0.001 TYR F 88 PHE 0.010 0.001 PHE L 149 TRP 0.013 0.001 TRP N 199 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (17096) covalent geometry : angle 0.61265 / 0.34 (24387) SS BOND : bond 0.00349 / 0.22 ( 4) SS BOND : angle 0.84893 / 1.05 ( 8) hydrogen bonds : bond 0.04006 / 4.30 ( 943) hydrogen bonds : angle 3.43030 / 4.33 ( 2398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8178 (pm20) REVERT: F 79 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8520 (mtmm) REVERT: F 84 MET cc_start: 0.9272 (mmm) cc_final: 0.8921 (mmm) REVERT: F 91 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8941 (ttmt) REVERT: G 41 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7909 (tm-30) REVERT: G 64 GLU cc_start: 0.9052 (tt0) cc_final: 0.8813 (tt0) REVERT: G 91 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: H 39 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8943 (t) REVERT: H 40 ILE cc_start: 0.9139 (tt) cc_final: 0.8683 (pp) REVERT: H 72 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8378 (tp30) REVERT: A 56 LYS cc_start: 0.9350 (ptmm) cc_final: 0.9019 (ptpp) REVERT: A 81 ASP cc_start: 0.8861 (m-30) cc_final: 0.8631 (p0) REVERT: A 99 TYR cc_start: 0.9487 (t80) cc_final: 0.9247 (t80) REVERT: A 133 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8594 (ttp80) REVERT: B 95 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7417 (mtp180) REVERT: C 73 ASN cc_start: 0.8595 (t0) cc_final: 0.8228 (t160) REVERT: C 91 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: C 95 LYS cc_start: 0.9143 (tmtm) cc_final: 0.8893 (ttmt) REVERT: D 69 ASP cc_start: 0.9178 (t70) cc_final: 0.8738 (t0) REVERT: N 23 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6792 (tp30) REVERT: N 64 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8531 (ttp-110) REVERT: N 65 GLN cc_start: 0.8728 (mp10) cc_final: 0.8417 (mp10) REVERT: N 95 ASP cc_start: 0.8404 (t0) cc_final: 0.7956 (t0) REVERT: K 42 MET cc_start: 0.8874 (mtm) cc_final: 0.8526 (mtp) REVERT: K 45 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8897 (tmtm) REVERT: K 64 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8414 (ttp80) REVERT: K 95 ASP cc_start: 0.8965 (t0) cc_final: 0.8706 (t0) REVERT: K 235 ASN cc_start: 0.8566 (p0) cc_final: 0.8232 (p0) outliers start: 41 outliers final: 14 residues processed: 237 average time/residue: 0.7641 time to fit residues: 196.4332 Evaluate side-chains 228 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.061547 restraints weight = 32981.608| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.62 r_work: 0.2743 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17100 Z= 0.195 Angle : 0.634 11.634 24395 Z= 0.352 Chirality : 0.044 0.283 2757 Planarity : 0.004 0.043 2046 Dihedral : 30.071 167.027 4685 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.82 % Allowed : 26.26 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1259 helix: 2.57 (0.21), residues: 612 sheet: 0.57 (0.34), residues: 236 loop : -0.76 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.013 0.001 TYR K 72 PHE 0.010 0.001 PHE L 149 TRP 0.007 0.001 TRP K 58 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (17096) covalent geometry : angle 0.63351 / 0.35 (24387) SS BOND : bond 0.00463 / 0.31 ( 4) SS BOND : angle 0.98747 / 1.32 ( 8) hydrogen bonds : bond 0.04400 / 4.71 ( 943) hydrogen bonds : angle 3.46095 / 4.35 ( 2398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8290 (pm20) REVERT: F 79 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8609 (mtmm) REVERT: F 84 MET cc_start: 0.9265 (mmm) cc_final: 0.8930 (mmm) REVERT: F 91 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8991 (ttmt) REVERT: G 41 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7920 (tm-30) REVERT: G 64 GLU cc_start: 0.9078 (tt0) cc_final: 0.8839 (tt0) REVERT: G 91 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: H 39 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.8989 (t) REVERT: A 56 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9079 (ptpp) REVERT: A 81 ASP cc_start: 0.8866 (m-30) cc_final: 0.8594 (p0) REVERT: A 133 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 24 ASP cc_start: 0.8077 (p0) cc_final: 0.7868 (p0) REVERT: B 92 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8547 (ttp80) REVERT: B 95 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7478 (mtp180) REVERT: C 73 ASN cc_start: 0.8652 (t0) cc_final: 0.8284 (t160) REVERT: C 91 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: C 95 LYS cc_start: 0.9176 (tmtm) cc_final: 0.8941 (ttmt) REVERT: D 69 ASP cc_start: 0.9276 (t70) cc_final: 0.8928 (t0) REVERT: N 23 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: N 64 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8476 (ttp-110) REVERT: N 95 ASP cc_start: 0.8509 (t0) cc_final: 0.8050 (t0) REVERT: K 42 MET cc_start: 0.8913 (mtm) cc_final: 0.8580 (mtp) REVERT: K 45 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8982 (tmtm) REVERT: K 95 ASP cc_start: 0.8963 (t0) cc_final: 0.8708 (t0) REVERT: K 235 ASN cc_start: 0.8613 (p0) cc_final: 0.8281 (p0) outliers start: 41 outliers final: 18 residues processed: 237 average time/residue: 0.7820 time to fit residues: 200.5237 Evaluate side-chains 230 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 0.0040 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063401 restraints weight = 33046.130| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.56 r_work: 0.2770 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17100 Z= 0.132 Angle : 0.607 11.630 24395 Z= 0.342 Chirality : 0.042 0.292 2757 Planarity : 0.004 0.046 2046 Dihedral : 29.953 167.590 4685 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 27.47 % Favored : 69.37 % 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: 1.87 (0.24), residues: 1259 helix: 2.70 (0.21), residues: 612 sheet: 0.55 (0.35), residues: 236 loop : -0.64 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.011 0.001 TYR F 88 PHE 0.010 0.001 PHE L 149 TRP 0.008 0.001 TRP N 199 HIS 0.003 0.001 HIS K 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (17096) covalent geometry : angle 0.60673 / 0.34 (24387) SS BOND : bond 0.00307 / 0.20 ( 4) SS BOND : angle 0.85318 / 1.04 ( 8) hydrogen bonds : bond 0.03903 / 4.21 ( 943) hydrogen bonds : angle 3.36739 / 4.25 ( 2398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.481 Fit side-chains REVERT: E 59 GLU cc_start: 0.8600 (pm20) cc_final: 0.8301 (pm20) REVERT: F 79 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8586 (mtmm) REVERT: F 84 MET cc_start: 0.9186 (mmm) cc_final: 0.8752 (mmm) REVERT: F 91 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8963 (ttmt) REVERT: G 41 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7878 (tm-30) REVERT: G 64 GLU cc_start: 0.9065 (tt0) cc_final: 0.8823 (tt0) REVERT: G 91 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: H 39 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8945 (t) REVERT: H 40 ILE cc_start: 0.9127 (tt) cc_final: 0.8738 (pt) REVERT: H 72 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8436 (tp30) REVERT: A 56 LYS cc_start: 0.9385 (ptmm) cc_final: 0.9070 (ptpp) REVERT: A 81 ASP cc_start: 0.8864 (m-30) cc_final: 0.8586 (p0) REVERT: A 133 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 92 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8610 (ttp80) REVERT: B 95 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8316 (mtp85) REVERT: C 73 ASN cc_start: 0.8615 (t0) cc_final: 0.8233 (t160) REVERT: C 95 LYS cc_start: 0.9178 (tmtm) cc_final: 0.8944 (ttmt) REVERT: C 104 GLN cc_start: 0.9049 (mm110) cc_final: 0.8822 (mm110) REVERT: D 69 ASP cc_start: 0.9210 (t70) cc_final: 0.8850 (t0) REVERT: N 23 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: N 64 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8488 (ttp-110) REVERT: N 65 GLN cc_start: 0.8637 (mp10) cc_final: 0.8263 (mp10) REVERT: N 95 ASP cc_start: 0.8482 (t0) cc_final: 0.8001 (t0) REVERT: N 162 MET cc_start: 0.9130 (mmm) cc_final: 0.8606 (mmm) REVERT: N 169 MET cc_start: 0.8823 (pmt) cc_final: 0.8091 (pmt) REVERT: N 176 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8001 (mmm-85) REVERT: K 42 MET cc_start: 0.8894 (mtm) cc_final: 0.8576 (mtp) REVERT: K 45 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8939 (tmtm) REVERT: K 64 ARG cc_start: 0.8631 (ttp80) cc_final: 0.7834 (ttp80) REVERT: K 65 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: K 95 ASP cc_start: 0.8959 (t0) cc_final: 0.8740 (t0) REVERT: K 139 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8922 (p) REVERT: K 235 ASN cc_start: 0.8547 (p0) cc_final: 0.8224 (p0) outliers start: 34 outliers final: 16 residues processed: 238 average time/residue: 0.7555 time to fit residues: 195.1939 Evaluate side-chains 234 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063190 restraints weight = 32994.621| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.48 r_work: 0.2759 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17100 Z= 0.157 Angle : 0.618 11.647 24395 Z= 0.346 Chirality : 0.043 0.311 2757 Planarity : 0.004 0.058 2046 Dihedral : 29.942 167.520 4685 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.45 % Allowed : 26.91 % Favored : 69.65 % 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: 1.84 (0.24), residues: 1259 helix: 2.70 (0.21), residues: 612 sheet: 0.61 (0.36), residues: 212 loop : -0.68 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 87 TYR 0.012 0.001 TYR K 72 PHE 0.010 0.001 PHE L 149 TRP 0.006 0.001 TRP N 199 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (17096) covalent geometry : angle 0.61816 / 0.35 (24387) SS BOND : bond 0.00356 / 0.24 ( 4) SS BOND : angle 0.88282 / 1.15 ( 8) hydrogen bonds : bond 0.04006 / 4.32 ( 943) hydrogen bonds : angle 3.37622 / 4.25 ( 2398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8308 (pm20) REVERT: F 79 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8599 (mtmm) REVERT: F 91 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8970 (ttmt) REVERT: G 64 GLU cc_start: 0.9079 (tt0) cc_final: 0.8833 (tt0) REVERT: G 91 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: H 39 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.9009 (t) REVERT: H 40 ILE cc_start: 0.9144 (tt) cc_final: 0.8723 (pp) REVERT: H 60 MET cc_start: 0.9027 (tpp) cc_final: 0.8707 (tpp) REVERT: H 72 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8401 (tp30) REVERT: A 56 LYS cc_start: 0.9396 (ptmm) cc_final: 0.9085 (ptpp) REVERT: A 81 ASP cc_start: 0.8879 (m-30) cc_final: 0.8595 (p0) REVERT: A 99 TYR cc_start: 0.9444 (t80) cc_final: 0.9195 (t80) REVERT: A 133 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 92 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8555 (ttp80) REVERT: B 95 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8340 (mtp85) REVERT: C 73 ASN cc_start: 0.8637 (t0) cc_final: 0.8252 (t160) REVERT: C 95 LYS cc_start: 0.9176 (tmtm) cc_final: 0.8942 (ttmt) REVERT: D 69 ASP cc_start: 0.9239 (t70) cc_final: 0.8813 (t0) REVERT: N 23 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: N 64 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8455 (ttp-110) REVERT: N 65 GLN cc_start: 0.8597 (mp10) cc_final: 0.8174 (mp10) REVERT: N 95 ASP cc_start: 0.8501 (t0) cc_final: 0.8021 (t0) REVERT: N 169 MET cc_start: 0.8844 (pmt) cc_final: 0.8113 (pmt) REVERT: K 42 MET cc_start: 0.8882 (mtm) cc_final: 0.8575 (mtp) REVERT: K 45 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8928 (tmtm) REVERT: K 95 ASP cc_start: 0.8960 (t0) cc_final: 0.8737 (t0) REVERT: K 139 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (p) REVERT: K 235 ASN cc_start: 0.8559 (p0) cc_final: 0.8237 (p0) outliers start: 37 outliers final: 20 residues processed: 231 average time/residue: 0.7648 time to fit residues: 191.6126 Evaluate side-chains 233 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 40.0000 chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.105545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062186 restraints weight = 33130.994| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.59 r_work: 0.2746 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17100 Z= 0.206 Angle : 0.642 11.668 24395 Z= 0.357 Chirality : 0.043 0.294 2757 Planarity : 0.004 0.051 2046 Dihedral : 29.988 167.494 4685 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.17 % Allowed : 27.47 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1259 helix: 2.65 (0.21), residues: 612 sheet: 0.57 (0.36), residues: 212 loop : -0.70 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 87 TYR 0.014 0.001 TYR K 72 PHE 0.009 0.001 PHE L 149 TRP 0.007 0.001 TRP K 58 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (17096) covalent geometry : angle 0.64142 / 0.36 (24387) SS BOND : bond 0.00452 / 0.32 ( 4) SS BOND : angle 0.98563 / 1.34 ( 8) hydrogen bonds : bond 0.04241 / 4.55 ( 943) hydrogen bonds : angle 3.41778 / 4.30 ( 2398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8609 (pm20) cc_final: 0.8259 (pm20) REVERT: F 79 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8606 (mtmm) REVERT: F 91 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8989 (ttmt) REVERT: G 64 GLU cc_start: 0.9091 (tt0) cc_final: 0.8849 (tt0) REVERT: G 91 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: H 39 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8994 (t) REVERT: H 72 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8399 (tp30) REVERT: A 56 LYS cc_start: 0.9404 (ptmm) cc_final: 0.9099 (ptpp) REVERT: A 81 ASP cc_start: 0.8898 (m-30) cc_final: 0.8607 (p0) REVERT: A 133 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 92 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: C 73 ASN cc_start: 0.8659 (t0) cc_final: 0.8279 (t160) REVERT: C 91 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: C 95 LYS cc_start: 0.9162 (tmtm) cc_final: 0.8937 (ttmt) REVERT: D 69 ASP cc_start: 0.9281 (t70) cc_final: 0.8944 (t0) REVERT: N 23 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: N 64 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8493 (ttp-110) REVERT: N 95 ASP cc_start: 0.8539 (t0) cc_final: 0.8054 (t0) REVERT: N 162 MET cc_start: 0.9135 (mmm) cc_final: 0.8847 (mmm) REVERT: N 169 MET cc_start: 0.8909 (pmt) cc_final: 0.8181 (pmt) REVERT: K 42 MET cc_start: 0.8924 (mtm) cc_final: 0.8608 (mtp) REVERT: K 45 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8982 (tmtm) REVERT: K 95 ASP cc_start: 0.8982 (t0) cc_final: 0.8724 (t0) REVERT: K 139 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8922 (p) REVERT: K 235 ASN cc_start: 0.8619 (p0) cc_final: 0.8302 (p0) outliers start: 34 outliers final: 18 residues processed: 223 average time/residue: 0.7972 time to fit residues: 192.2691 Evaluate side-chains 228 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 8 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 14 optimal weight: 50.0000 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 73 ASN A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063516 restraints weight = 32858.753| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.53 r_work: 0.2775 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17100 Z= 0.133 Angle : 0.619 11.588 24395 Z= 0.347 Chirality : 0.042 0.291 2757 Planarity : 0.004 0.047 2046 Dihedral : 29.925 167.799 4685 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 27.19 % Favored : 69.65 % 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: 1.91 (0.24), residues: 1259 helix: 2.74 (0.21), residues: 612 sheet: 0.67 (0.36), residues: 212 loop : -0.63 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 64 TYR 0.010 0.001 TYR N 72 PHE 0.009 0.001 PHE L 149 TRP 0.007 0.001 TRP N 199 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (17096) covalent geometry : angle 0.61923 / 0.35 (24387) SS BOND : bond 0.00320 / 0.20 ( 4) SS BOND : angle 0.83027 / 1.03 ( 8) hydrogen bonds : bond 0.03887 / 4.19 ( 943) hydrogen bonds : angle 3.35104 / 4.23 ( 2398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6634.53 seconds wall clock time: 113 minutes 34.44 seconds (6814.44 seconds total)